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Repository: nf-core/atacseq
Branch: master
Commit: 1a1dbe52ffbd
Files: 204
Total size: 1.0 MB
Directory structure:
gitextract_tbgkhg71/
├── .devcontainer/
│ └── devcontainer.json
├── .editorconfig
├── .gitattributes
├── .github/
│ ├── .dockstore.yml
│ ├── CONTRIBUTING.md
│ ├── ISSUE_TEMPLATE/
│ │ ├── bug_report.yml
│ │ ├── config.yml
│ │ └── feature_request.yml
│ ├── PULL_REQUEST_TEMPLATE.md
│ └── workflows/
│ ├── awsfulltest.yml
│ ├── awstest.yml
│ ├── branch.yml
│ ├── ci.yml
│ ├── clean-up.yml
│ ├── fix-linting.yml
│ ├── linting.yml
│ └── linting_comment.yml
├── .gitignore
├── .gitpod.yml
├── .nf-core.yml
├── .pre-commit-config.yaml
├── .prettierignore
├── .prettierrc.yml
├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets/
│ ├── adaptivecard.json
│ ├── bamtools_filter_pe.json
│ ├── bamtools_filter_se.json
│ ├── blacklists/
│ │ ├── old/
│ │ │ ├── GRCm38-blacklist.bed
│ │ │ ├── hg38-blacklist.bed
│ │ │ └── mm10-blacklist.bed
│ │ ├── v1.0/
│ │ │ ├── GRCh37-blacklist.v1.bed
│ │ │ └── hg19-blacklist.v1.bed
│ │ ├── v2.0/
│ │ │ ├── GRCm38-blacklist.v2.bed
│ │ │ ├── ce10-blacklist.v2.bed
│ │ │ ├── ce11-blacklist.v2.bed
│ │ │ ├── dm3-blacklist.v2.bed
│ │ │ ├── dm6-blacklist.v2.bed
│ │ │ ├── hg19-blacklist.v2.bed
│ │ │ ├── hg38-blacklist.v2.bed
│ │ │ └── mm10-blacklist.v2.bed
│ │ └── v3.0/
│ │ ├── GRCh38-blacklist.v3.bed
│ │ └── hg38-blacklist.v3.bed
│ ├── email_template.html
│ ├── email_template.txt
│ ├── methods_description_template.yml
│ ├── multiqc/
│ │ ├── merged_library_deseq2_clustering_header.txt
│ │ ├── merged_library_deseq2_pca_header.txt
│ │ ├── merged_library_frip_score_header.txt
│ │ ├── merged_library_peak_annotation_header.txt
│ │ ├── merged_library_peak_count_header.txt
│ │ ├── merged_replicate_deseq2_clustering_header.txt
│ │ ├── merged_replicate_deseq2_pca_header.txt
│ │ ├── merged_replicate_frip_score_header.txt
│ │ ├── merged_replicate_peak_annotation_header.txt
│ │ └── merged_replicate_peak_count_header.txt
│ ├── multiqc_config.yml
│ ├── samplesheet.csv
│ ├── schema_input.json
│ ├── sendmail_template.txt
│ └── slackreport.json
├── bin/
│ ├── bampe_rm_orphan.py
│ ├── check_samplesheet.py
│ ├── deseq2_qc.r
│ ├── get_autosomes.py
│ ├── gtf2bed
│ ├── igv_files_to_session.py
│ ├── macs2_merged_expand.py
│ ├── plot_homer_annotatepeaks.r
│ ├── plot_macs2_qc.r
│ └── plot_peak_intersect.r
├── conf/
│ ├── base.config
│ ├── igenomes.config
│ ├── modules.config
│ ├── test.config
│ ├── test_controls.config
│ └── test_full.config
├── docs/
│ ├── README.md
│ ├── output.md
│ └── usage.md
├── lib/
│ ├── NfcoreTemplate.groovy
│ ├── Utils.groovy
│ ├── WorkflowAtacseq.groovy
│ ├── WorkflowMain.groovy
│ └── nfcore_external_java_deps.jar
├── main.nf
├── modules/
│ ├── local/
│ │ ├── bam_remove_orphans.nf
│ │ ├── bamtools_filter.nf
│ │ ├── bedtools_genomecov.nf
│ │ ├── deseq2_qc.nf
│ │ ├── frip_score.nf
│ │ ├── genome_blacklist_regions.nf
│ │ ├── get_autosomes.nf
│ │ ├── gtf2bed.nf
│ │ ├── igv.nf
│ │ ├── macs2_consensus.nf
│ │ ├── multiqc.nf
│ │ ├── multiqc_custom_peaks.nf
│ │ ├── plot_homer_annotatepeaks.nf
│ │ ├── plot_macs2_qc.nf
│ │ ├── samplesheet_check.nf
│ │ ├── star_align.nf
│ │ ├── star_genomegenerate.nf
│ │ └── tss_extract.nf
│ └── nf-core/
│ ├── ataqv/
│ │ ├── ataqv/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── mkarv/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bowtie2/
│ │ ├── align/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── build/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bwa/
│ │ ├── index/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── mem/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── chromap/
│ │ ├── chromap/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── index/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── custom/
│ │ ├── dumpsoftwareversions/
│ │ │ ├── main.nf
│ │ │ ├── meta.yml
│ │ │ └── templates/
│ │ │ └── dumpsoftwareversions.py
│ │ └── getchromsizes/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── deeptools/
│ │ ├── computematrix/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── plotfingerprint/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── plotheatmap/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── plotprofile/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastqc/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── gffread/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── gunzip/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── homer/
│ │ └── annotatepeaks/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── khmer/
│ │ └── uniquekmers/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── macs2/
│ │ └── callpeak/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── picard/
│ │ ├── collectmultiplemetrics/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── markduplicates/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── mergesamfiles/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── preseq/
│ │ └── lcextrap/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── samtools/
│ │ ├── flagstat/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── idxstats/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── index/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── sort/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── stats/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── subread/
│ │ └── featurecounts/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── trimgalore/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── ucsc/
│ │ └── bedgraphtobigwig/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── umitools/
│ │ └── extract/
│ │ ├── main.nf
│ │ └── meta.yml
│ └── untar/
│ ├── main.nf
│ └── meta.yml
├── modules.json
├── nextflow.config
├── nextflow_schema.json
├── pyproject.toml
├── subworkflows/
│ ├── local/
│ │ ├── align_star.nf
│ │ ├── bam_bedgraph_bigwig_bedtools_ucsc.nf
│ │ ├── bam_filter_bamtools.nf
│ │ ├── bam_peaks_call_qc_annotate_macs2_homer.nf
│ │ ├── bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf
│ │ ├── bigwig_plot_deeptools.nf
│ │ ├── input_check.nf
│ │ └── prepare_genome.nf
│ └── nf-core/
│ ├── bam_markduplicates_picard/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bam_sort_stats_samtools/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bam_stats_samtools/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastq_align_bowtie2/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastq_align_bwa/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastq_align_chromap/
│ │ ├── main.nf
│ │ └── meta.yml
│ └── fastq_fastqc_umitools_trimgalore/
│ ├── main.nf
│ └── meta.yml
├── tower.yml
└── workflows/
└── atacseq.nf
================================================
FILE CONTENTS
================================================
================================================
FILE: .devcontainer/devcontainer.json
================================================
{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
},
// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}
================================================
FILE: .editorconfig
================================================
root = true
[*]
charset = utf-8
end_of_line = lf
insert_final_newline = true
trim_trailing_whitespace = true
indent_size = 4
indent_style = space
[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2
# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset
[/assets/email*]
indent_size = unset
[/assets/blacklists/GRCh37-blacklist.bed]
trim_trailing_whitespace = unset
================================================
FILE: .gitattributes
================================================
*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
================================================
FILE: .github/.dockstore.yml
================================================
# Dockstore config version, not pipeline version
version: 1.2
workflows:
- subclass: nfl
primaryDescriptorPath: /nextflow.config
publish: True
================================================
FILE: .github/CONTRIBUTING.md
================================================
# nf-core/atacseq: Contributing Guidelines
Hi there!
Many thanks for taking an interest in improving nf-core/atacseq.
We try to manage the required tasks for nf-core/atacseq using GitHub issues, you probably came to this page when creating one.
Please use the pre-filled template to save time.
However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)
> If you need help using or modifying nf-core/atacseq then the best place to ask is on the nf-core Slack [#atacseq](https://nfcore.slack.com/channels/atacseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
## Contribution workflow
If you'd like to write some code for nf-core/atacseq, the standard workflow is as follows:
1. Check that there isn't already an issue about your idea in the [nf-core/atacseq issues](https://github.com/nf-core/atacseq/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/atacseq repository](https://github.com/nf-core/atacseq) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
## Tests
When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
There are typically two types of tests that run:
### Lint tests
`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
If any failures or warnings are encountered, please follow the listed URL for more documentation.
### Pipeline tests
Each `nf-core` pipeline should be set up with a minimal set of test-data.
`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
If there are any failures then the automated tests fail.
These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
## Patch
:warning: Only in the unlikely and regretful event of a release happening with a bug.
- On your own fork, make a new branch `patch` based on `upstream/master`.
- Fix the bug, and bump version (X.Y.Z+1).
- A PR should be made on `master` from patch to directly this particular bug.
## Getting help
For further information/help, please consult the [nf-core/atacseq documentation](https://nf-co.re/atacseq/usage) and don't hesitate to get in touch on the nf-core Slack [#atacseq](https://nfcore.slack.com/channels/atacseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
## Pipeline contribution conventions
To make the nf-core/atacseq code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
### Adding a new step
If you wish to contribute a new step, please use the following coding standards:
1. Define the corresponding input channel into your new process from the expected previous process channel
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new parameters to `nextflow.config` with a default (see below).
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
### Default values
Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.
Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
### Default processes resource requirements
Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
### Naming schemes
Please use the following naming schemes, to make it easy to understand what is going where.
- initial process channel: `ch_output_from_<process>`
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
### Nextflow version bumping
If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
### Images and figures
For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
## GitHub Codespaces
This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
To get started:
- Open the repo in [Codespaces](https://github.com/nf-core/atacseq/codespaces)
- Tools installed
- nf-core
- Nextflow
Devcontainer specs:
- [DevContainer config](.devcontainer/devcontainer.json)
================================================
FILE: .github/ISSUE_TEMPLATE/bug_report.yml
================================================
name: Bug report
description: Report something that is broken or incorrect
labels: bug
body:
- type: markdown
attributes:
value: |
Before you post this issue, please check the documentation:
- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [nf-core/atacseq pipeline documentation](https://nf-co.re/atacseq/usage)
- type: textarea
id: description
attributes:
label: Description of the bug
description: A clear and concise description of what the bug is.
validations:
required: true
- type: textarea
id: command_used
attributes:
label: Command used and terminal output
description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
render: console
placeholder: |
$ nextflow run ...
Some output where something broke
- type: textarea
id: files
attributes:
label: Relevant files
description: |
Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
- type: textarea
id: system
attributes:
label: System information
description: |
* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of nf-core/atacseq _(eg. 1.1, 1.5, 1.8.2)_
================================================
FILE: .github/ISSUE_TEMPLATE/config.yml
================================================
contact_links:
- name: Join nf-core
url: https://nf-co.re/join
about: Please join the nf-core community here
- name: "Slack #atacseq channel"
url: https://nfcore.slack.com/channels/atacseq
about: Discussion about the nf-core/atacseq pipeline
================================================
FILE: .github/ISSUE_TEMPLATE/feature_request.yml
================================================
name: Feature request
description: Suggest an idea for the nf-core/atacseq pipeline
labels: enhancement
body:
- type: textarea
id: description
attributes:
label: Description of feature
description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
validations:
required: true
================================================
FILE: .github/PULL_REQUEST_TEMPLATE.md
================================================
<!--
# nf-core/atacseq pull request
Many thanks for contributing to nf-core/atacseq!
Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/atacseq/tree/master/.github/CONTRIBUTING.md)
-->
## PR checklist
- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/atacseq/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/atacseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and authors/contributors).
================================================
FILE: .github/workflows/awsfulltest.yml
================================================
name: nf-core AWS full size tests
# This workflow is triggered on published releases.
# It can be additionally triggered manually with GitHub actions workflow dispatch button.
# It runs the -profile 'test_full' on AWS batch
on:
release:
types: [published]
workflow_dispatch:
jobs:
run-tower:
name: Run AWS full tests
if: github.repository == 'nf-core/atacseq'
runs-on: ubuntu-latest
strategy:
matrix:
aligner: ["bwa", "bowtie2", "chromap", "star"]
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/atacseq/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/atacseq/results-${{ github.sha }}",
"aligner": "${{ matrix.aligner }}"
}
profiles: test_full
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
================================================
FILE: .github/workflows/awstest.yml
================================================
name: nf-core AWS test
# This workflow can be triggered manually with the GitHub actions workflow dispatch button.
# It runs the -profile 'test' on AWS batch
on:
workflow_dispatch:
jobs:
run-tower:
name: Run AWS tests
if: github.repository == 'nf-core/atacseq'
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/atacseq/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/atacseq/results-test-${{ github.sha }}"
}
profiles: test
- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
================================================
FILE: .github/workflows/branch.yml
================================================
name: nf-core branch protection
# This workflow is triggered on PRs to master branch on the repository
# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
on:
pull_request_target:
branches: [master]
jobs:
test:
runs-on: ubuntu-latest
steps:
# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
- name: Check PRs
if: github.repository == 'nf-core/atacseq'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/atacseq ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
# If the above check failed, post a comment on the PR explaining the failure
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
with:
message: |
## This PR is against the `master` branch :x:
* Do not close this PR
* Click _Edit_ and change the `base` to `dev`
* This CI test will remain failed until you push a new commit
---
Hi @${{ github.event.pull_request.user.login }},
It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
The `master` branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false
================================================
FILE: .github/workflows/ci.yml
================================================
name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
test_controls:
name: Run pipeline with test data and controls
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}"
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
- name: Run pipeline with test data and controls
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_controls,docker --outdir ./results
parameters:
name: Test workflow parameters
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/atacseq') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_trimming"
- "--skip_merge_replicates"
- "--skip_consensus_peaks"
- "--aligner bowtie2"
- "--aligner chromap"
- "--aligner star"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Run pipeline with various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
================================================
FILE: .github/workflows/clean-up.yml
================================================
name: "Close user-tagged issues and PRs"
on:
schedule:
- cron: "0 0 * * 0" # Once a week
jobs:
clean-up:
runs-on: ubuntu-latest
permissions:
issues: write
pull-requests: write
steps:
- uses: actions/stale@v7
with:
stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
days-before-stale: 30
days-before-close: 20
days-before-pr-close: -1
any-of-labels: "awaiting-changes,awaiting-feedback"
exempt-issue-labels: "WIP"
exempt-pr-labels: "WIP"
repo-token: "${{ secrets.GITHUB_TOKEN }}"
================================================
FILE: .github/workflows/fix-linting.yml
================================================
name: Fix linting from a comment
on:
issue_comment:
types: [created]
jobs:
deploy:
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
if: >
contains(github.event.comment.html_url, '/pull/') &&
contains(github.event.comment.body, '@nf-core-bot fix linting') &&
github.repository == 'nf-core/atacseq'
runs-on: ubuntu-latest
steps:
# Use the @nf-core-bot token to check out so we can push later
- uses: actions/checkout@v3
with:
token: ${{ secrets.nf_core_bot_auth_token }}
# Action runs on the issue comment, so we don't get the PR by default
# Use the gh cli to check out the PR
- name: Checkout Pull Request
run: gh pr checkout ${{ github.event.issue.number }}
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
- uses: actions/setup-node@v3
- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
# Check that we actually need to fix something
- name: Run 'prettier --check'
id: prettier_status
run: |
if prettier --check ${GITHUB_WORKSPACE}; then
echo "result=pass" >> $GITHUB_OUTPUT
else
echo "result=fail" >> $GITHUB_OUTPUT
fi
- name: Run 'prettier --write'
if: steps.prettier_status.outputs.result == 'fail'
run: prettier --write ${GITHUB_WORKSPACE}
- name: Commit & push changes
if: steps.prettier_status.outputs.result == 'fail'
run: |
git config user.email "core@nf-co.re"
git config user.name "nf-core-bot"
git config push.default upstream
git add .
git status
git commit -m "[automated] Fix linting with Prettier"
git push
================================================
FILE: .github/workflows/linting.yml
================================================
name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-node@v3
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-node@v3
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Check code lints with Black
uses: psf/black@stable
# If the above check failed, post a comment on the PR explaining the failure
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
with:
message: |
## Python linting (`black`) is failing
To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:
* Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
* Fix formatting errors in your pipeline: `black .`
Once you push these changes the test should pass, and you can hide this comment :+1:
We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false
nf-core:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
- uses: actions/setup-python@v4
with:
python-version: "3.8"
architecture: "x64"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install nf-core
- name: Run nf-core lint
env:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
- name: Save PR number
if: ${{ always() }}
run: echo ${{ github.event.pull_request.number }} > PR_number.txt
- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@v3
with:
name: linting-logs
path: |
lint_log.txt
lint_results.md
PR_number.txt
================================================
FILE: .github/workflows/linting_comment.yml
================================================
name: nf-core linting comment
# This workflow is triggered after the linting action is complete
# It posts an automated comment to the PR, even if the PR is coming from a fork
on:
workflow_run:
workflows: ["nf-core linting"]
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: Download lint results
uses: dawidd6/action-download-artifact@v2
with:
workflow: linting.yml
workflow_conclusion: completed
- name: Get PR number
id: pr_number
run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
- name: Post PR comment
uses: marocchino/sticky-pull-request-comment@v2
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }}
path: linting-logs/lint_results.md
================================================
FILE: .gitignore
================================================
.nextflow*
work/
data/
results/
.DS_Store
testing/
testing*
*.pyc
================================================
FILE: .gitpod.yml
================================================
image: nfcore/gitpod:latest
tasks:
- name: Update Nextflow and setup pre-commit
command: |
pre-commit install --install-hooks
nextflow self-update
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code
================================================
FILE: .nf-core.yml
================================================
repository_type: pipeline
================================================
FILE: .pre-commit-config.yaml
================================================
repos:
- repo: https://github.com/pre-commit/mirrors-prettier
rev: "v2.7.1"
hooks:
- id: prettier
================================================
FILE: .prettierignore
================================================
email_template.html
adaptivecard.json
slackreport.json
.nextflow*
work/
data/
results/
.DS_Store
testing/
testing*
*.pyc
bin/
================================================
FILE: .prettierrc.yml
================================================
printWidth: 120
================================================
FILE: CHANGELOG.md
================================================
# nf-core/atacseq: Changelog
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [[2.1.2](https://github.com/nf-core/atacseq/releases/tag/2.1.2)] - 2022-08-07
### Enhancements & fixes
- [[#322](https://github.com/nf-core/atacseq/issues/322)]Remove fasta from required schema parameters so that when launching from tools it is not required.
- Updates `homer_annotatepeaks` module.
## [[2.1.1](https://github.com/nf-core/atacseq/releases/tag/2.1.1)] - 2022-07-21
- Minor patch release to fix AWS full test.
## [[2.1.0](https://github.com/nf-core/atacseq/releases/tag/2.1.0)] - 2022-07-21
### Credits
Special thanks to the following for their contributions to the release:
- [Adam Talbot](https://github.com/adamrtalbot)
- [Björn Langer](https://github.com/bjlang)
- [Harshil Patel](https://github.com/drpatelh)
- [Maxime Garcia](https://github.com/maxulysse)
- [Rob Syme](https://github.com/robsyme)
Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
### Enhancements & fixes
- [[#226](https://github.com/nf-core/atacseq/issues/262)] - Add `ataqv_mito_reference` parameter.
- Optional support of control data analog to nf-core/chipseq.
- [[#277](https://github.com/nf-core/atacseq/issues/277)] - Fix error when using a gunziped fasta file.
- [[#286](https://github.com/nf-core/atacseq/issues/286)] - Fix error when no `--mito_name parameter is provided.
- [[#268](https://github.com/nf-core/atacseq/issues/268)] - Fix error when a bed file is provided using the `--blacklist` option.
- [[#278](https://github.com/nf-core/atacseq/issues/278)] - Make genome fasta file available when `IGV` process is run.
- [[#276](https://github.com/nf-core/atacseq/issues/276)] - Bump version 1.3.1 of ataqv to fix enrichment plots rendering.
- [[#290](https://github.com/nf-core/atacseq/issues/290)] - Fix case-sensitivity issue while sorting bedGraph.
- [[#295](https://github.com/nf-core/atacseq/issues/295)] - Enable downstream steps for bam files produced from paired-end reads by `chromap` after its upgrade.
- Updated pipeline template to [nf-core/tools 2.9](https://github.com/nf-core/tools/releases/tag/2.9)
- Make fasta index available for IGV session.
- [[nf-core/chipseq#347](https://github.com/nf-core/chipseq/issues/347)] - Add read group tag to bam files processed by bowtie2
### Parameters
| Old parameter | New parameter |
| ------------- | ------------------------ |
| | `--with_control` |
| | `--ataqv_mito_reference` |
> **NB:** Parameter has been **updated** if both old and new parameter information is present.
> **NB:** Parameter has been **added** if just the new parameter information is present.
> **NB:** Parameter has been **removed** if parameter information isn't present.
### Software dependencies
Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
| Dependency | Old version | New version |
| ----------------------- | ----------- | ----------- |
| `ataqv` | 1.3.0 | 1.3.1 |
| `chromap` | 0.2.1 | 0.2.4 |
| `multiqc` | 1.13 | 1.14 |
| `picard` | 2.27.4 | 3.0.0 |
| `samtools` | 1.15.1 | 1.17 |
| `ucsc-bedgraphtobigwig` | 377 | 445 |
> **NB:** Dependency has been **updated** if both old and new version information is present.
> **NB:** Dependency has been **added** if just the new version information is present.
> **NB:** Dependency has been **removed** if version information isn't present.
## [[2.0](https://github.com/nf-core/atacseq/releases/tag/2.0)] - 2022-11-30
### :warning: Major enhancements
- Samplesheet format has changed from `group,replicate,fastq_1,fastq_2` to `sample,fastq_1,fastq_2,replicate`.
- This is primarily because we have removed the differential accessibility from the pipeline in favour of using more formal statistical methods downstream with the pipeline results. We kept replicate information as mandatory to merge samples at the replicate level to improve coverage for footprinting analysis.
- Pipeline has been re-implemented in [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html)
- Bump minimum Nextflow version from `19.10.0` -> `21.10.3`
- Updated pipeline template to [nf-core/tools 2.6](https://github.com/nf-core/tools/releases/tag/2.6)
- [[#135](https://github.com/nf-core/atacseq/issues/135)] - ERROR: Please check design file header
- [[#158](https://github.com/nf-core/atacseq/issues/158)] - Problem using hyphens in group names
- [[#182](https://github.com/nf-core/atacseq/issues/182)] - Update `macs_gsize` in `igenomes.config`, create a new `--read_length` parameter and implement the logic to calculate `--macs_gsize` when the parameter is missing
- [[#193](https://github.com/nf-core/atacseq/issues/193)] - TSS heatmap inconsistency between ChIPseeker and nf-core ATAC-seq pipeline
- [[#201](https://github.com/nf-core/atacseq/issues/201)] - Update blacklist bed files.
- [[#220](https://github.com/nf-core/atacseq/issues/220)] - Move FastQ files for minimal tests to S3
- [[nf-core/chipseq#160](https://github.com/nf-core/chipseq/issues/160)] - Add `bowtie2` and `star` as available aligners, via the `--aligner` parameter
- [[nf-core/chipseq#233](https://github.com/nf-core/chipseq/issues/233)] - Add `chromap` to the available aligners
- Add `--save_unaligned` parameter (only available for `bowtie2` and `star`)
- Preseq will be skipped by default (see [nf-core/rnaseq#897](https://github.com/nf-core/rnaseq/issues/897))
- `--deseq2_vst` will be turned on by default
### Parameters
| Old parameter | New parameter |
| ---------------------- | ------------------ |
| `--clusterOptions` | |
| `--conda` | `--enable_conda` |
| | `--skip_qc` |
| | `--aligner` |
| | `--save_unaligned` |
| | `--bowtie2_index` |
| | `--chromap_index` |
| | `--star_index` |
| `--skip_diff_analysis` | `--skip_deseq2_qc` |
| `--single_end` | |
| | `--read_length` |
> **NB:** Parameter has been **updated** if both old and new parameter information is present.
> **NB:** Parameter has been **added** if just the new parameter information is present.
> **NB:** Parameter has been **removed** if parameter information isn't present.
### Software dependencies
Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
| Dependency | Old version | New version |
| ----------------------- | ----------- | ----------- |
| `ataqv` | 1.1.1 | 1.3.0 |
| `bamtools` | 2.5.1 | 2.5.2 |
| `bedtools` | 2.29.2 | 2.30.0 |
| `bioconductor-deseq2` | 1.26.0 | 1.28.0 |
| `deeptools` | 3.4.3 | 3.5.1 |
| `multiqc` | 1.9 | 1.13 |
| `ucsc-bedgraphtobigwig` | 357 | 377 |
| `samtools` | 1.10 | 1.16.1 |
| `picard` | 2.23.1 | 2.27.4 |
| `preseq` | 2.0.3 | 3.1.2 |
| `pysam` | 0.15.3 | 0.19.0 |
| `r-base` | 3.6.1 | 4.0.3 |
| `r-ggplot2` | 3.3.2 | 3.3.3 |
| `trim-galore` | 0.6.5 | 0.6.7 |
| `khmer` | - | 3.0.0a3 |
| `r-optparse` | - | 1.7.1 |
| `r-tidyr` | - | - |
| `r-lattice` | - | - |
| `r-xfun` | - | - |
| `bioconductor-vsn` | - | - |
> **NB:** Dependency has been **updated** if both old and new version information is present.
> **NB:** Dependency has been **added** if just the new version information is present.
> **NB:** Dependency has been **removed** if version information isn't present.
## [1.2.2] - 2022-05-12
- Minor patch release to fix Conda environment and enable DSL1 by default in the `nextflow.config`.
### `Dependencies`
- Update r-base `3.6.2` -> `3.6.3`
- Update r-xfun `0.15` -> `0.22`
## [1.2.1] - 2020-07-29
- [#118](https://github.com/nf-core/atacseq/issues/118) - Minor patch release to update pipeline schema
## [1.2.0] - 2020-07-02
### `Added`
- [#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
- [#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report
- [#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2
- [#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2
- [#80](https://github.com/nf-core/atacseq/pull/80) - Added social preview image
- [#97](https://github.com/nf-core/atacseq/issues/97) - PBC1, PBC2 from pipeline?
- [#107](https://github.com/nf-core/atacseq/issues/107) - Add options to change MACS2 parameters
- [nf-core/chipseq#153](https://github.com/nf-core/chipseq/issues/153) - Add plotHeatmap
- [nf-core/chipseq#159](https://github.com/nf-core/chipseq/issues/159) - expose bwa mem -T parameter
- Regenerated screenshots and added collapsible sections for output files in `docs/output.md`
- Update template to tools `1.9`
- Replace `set` with `tuple` and `file()` with `path()` in all processes
- Capitalise process names
- Parameters:
- `--bwa_min_score` to set minimum alignment score for BWA MEM
- `--macs_fdr` to provide FDR threshold for MACS2 peak calling
- `--macs_pvalue` to provide p-value threshold for MACS2 peak calling
- `--skip_peak_qc` to skip MACS2 peak QC plot generation
- `--skip_peak_annotation` to skip annotation of MACS2 and consensus peaks with HOMER
- `--skip_consensus_peaks` to skip consensus peak generation
- `--deseq2_vst` to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
- `--publish_dir_mode` to customise method of publishing results to output directory [nf-core/tools#585](https://github.com/nf-core/tools/issues/585)
### `Fixed`
- [#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
- [#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
- [#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script
- [#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r
- [#110](https://github.com/nf-core/atacseq/pull/110) - updated AWS test GitHub actions
- [#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf?
- [nf-core/chipseq#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
- [nf-core/chipseq#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
- [nf-core/chipseq#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped
- Make executables in `bin/` compatible with Python 3
### `Dependencies`
- Add bioconductor-biocparallel `1.20.0`
- Add markdown `3.2.2`
- Add pigz `2.3.4`
- Add pygments `2.6.1`
- Add pymdown-extensions `7.1`
- Add python `3.7.6`
- Add r-reshape2 `1.4.4`
- Add r-tidyr `1.1.0`
- Update ataqv `1.0.0` -> `1.1.1`
- Update bedtools `2.27.1` -> `2.29.2`
- Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
- Update bioconductor-vsn `3.46.0` -> `3.54.0`
- Update deeptools `3.2.1` -> `3.4.3`
- Update fastqc `0.11.8` -> `0.11.9`
- Update gawk `4.2.1` -> `5.1.0`
- Update homer `4.9.1` -> `4.11`
- Update macs2 `2.1.2` -> `2.2.7.1`
- Update multiqc `1.7` -> `1.8`
- Update picard `2.19.0` -> `2.23.1`
- Update pysam `0.15.2` -> `0.15.3`
- Update r-base `3.4.1` -> `3.6.2`
- Update r-ggplot2 `3.1.0` -> `3.3.2`
- Update r-lattice `0.20_35` -> `0.20_41`
- Update r-optparse `1.6.0` -> `1.6.6`
- Update r-pheatmap `1.0.10` -> `1.0.12`
- Update r-scales `1.0.0` -> `1.1.1`
- Update r-upsetr `1.3.3` -> `1.4.0`
- Update r-xfun `0.3` -> `0.15`
- Update samtools `1.9` -> `1.10`
- Update subread `1.6.4` -> `2.0.1`
- Update trim-galore `0.5.0` -> `0.6.5`
- Update ucsc-bedgraphtobigwig `377` -> `357`
## [1.1.0] - 2019-11-05
### `Added`
- [#35](https://github.com/nf-core/atacseq/issues/35) - Add deepTools plotFingerprint
- [#46](https://github.com/nf-core/atacseq/issues/46) - Missing gene_bed path in igenomes config
- Merged in TEMPLATE branch for automated syncing
- Update template to tools `1.7`
- Add `CITATIONS.md` file
- Capitalised process names
- Add parameters:
- `--seq_center`
- `--trim_nextseq`
- `--fingerprint_bins`
- `--broad_cutoff`
- `--min_reps_consensus`
- `--save_macs_pileup`
- `--skip_diff_analysis`
- `--skip_*` for skipping QC steps
### `Fixed`
- **Change all parameters from `camelCase` to `snake_case` (see [Deprecated](#deprecated))**
- [#41](https://github.com/nf-core/atacseq/issues/41) - Docs: Add example plot images
- [#44](https://github.com/nf-core/atacseq/issues/44) - Output directory missing: macs2/consensus/deseq2
- [#45](https://github.com/nf-core/atacseq/issues/45) - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
- [#46](https://github.com/nf-core/atacseq/issues/46) - Stage blacklist file in channel properly
- [#50](https://github.com/nf-core/atacseq/issues/50) - HOMER number of peaks does not correspond to found MACS2 peaks
- Fixed bug in UpSetR peak intersection plot
- IGV now uses relative instead of absolute paths
- Smaller logo for completion email
- Renamed all channels to start with `ch_` prefix
- Increase default resource requirements in `base.config`
- Increase process-specific requirements based on user-reported failures
### `Dependencies`
- Update Nextflow `0.32.0` -> `19.10.0`
- Add preseq `2.0.3`
- Add deeptools `3.2.1`
- Add r-xfun `0.3`
- Add gawk `4.2.1`
### `Deprecated`
| Deprecated | Replacement |
| ---------------------------- | ------------------------- |
| `--design` | `--input` |
| `--singleEnd` | `--single_end` |
| `--saveGenomeIndex` | `--save_reference` |
| `--skipTrimming` | `--skip_trimming` |
| `--saveTrimmed` | `--save_trimmed` |
| `--keepMito` | `--keep_mito` |
| `--keepDups` | `--keep_dups` |
| `--keepMultiMap` | `--keep_multi_map` |
| `--skipMergeReplicates` | `--skip_merge_replicates` |
| `--saveAlignedIntermediates` | `--save_align_intermeds` |
| `--narrowPeak` | `--narrow_peak` |
## [1.0.0] - 2019-04-09
### `Added`
Initial release of nf-core/atacseq
Created with version 1.1 of the [nf-core](http://nf-co.re/) template.
================================================
FILE: CITATIONS.md
================================================
# nf-core/atacseq: Citations
## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
## Pipeline tools
- [BWA](https://www.ncbi.nlm.nih.gov/pubmed/19451168/)
> Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PubMed PMID: 19451168; PubMed Central PMCID: PMC2705234.
- [BEDTools](https://www.ncbi.nlm.nih.gov/pubmed/20110278/)
> Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824.
- [BamTools](https://www.ncbi.nlm.nih.gov/pubmed/21493652/)
> Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14. PubMed PMID: 21493652; PubMed Central PMCID: PMC3106182.
- [deepTools](https://www.ncbi.nlm.nih.gov/pubmed/27079975/)
> Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13. PubMed PMID: 27079975; PubMed Central PMCID: PMC4987876.
- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
- [featureCounts](https://www.ncbi.nlm.nih.gov/pubmed/24227677/)
> Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.
- [HOMER](https://www.ncbi.nlm.nih.gov/pubmed/20513432/)
> Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010 May 28;38(4):576-89. doi: 10.1016/j.molcel.2010.05.004. PubMed PMID: 20513432; PubMed Central PMCID: PMC2898526.
- [MACS2](https://www.ncbi.nlm.nih.gov/pubmed/18798982/)
> Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. PubMed PMID: 18798982; PubMed Central PMCID: PMC2592715.
- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
- [picard-tools](http://broadinstitute.github.io/picard)
- [preseq](https://www.ncbi.nlm.nih.gov/pubmed/23435259/)
> Daley T, Smith AD. Predicting the molecular complexity of sequencing libraries. Nat Methods. 2013 Apr;10(4):325-7. doi: 10.1038/nmeth.2375. Epub 2013 Feb 24. PubMed PMID: 23435259; PubMed Central PMCID: PMC3612374.
- [pysam](https://github.com/pysam-developers/pysam)
- [SAMtools](https://www.ncbi.nlm.nih.gov/pubmed/19505943/)
> Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002.
- [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
- [UCSC tools](https://www.ncbi.nlm.nih.gov/pubmed/20639541/)
> Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.
- [ataqv](https://github.com/ParkerLab/ataqv)
## R packages
- [R](https://www.R-project.org/)
> R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
- [DESeq2](https://www.ncbi.nlm.nih.gov/pubmed/25516281/)
> Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. PubMed PMID: 25516281; PubMed Central PMCID: PMC4302049.
- [UpSetR](https://CRAN.R-project.org/package=UpSetR)
> Nils Gehlenborg (2017). UpSetR: A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets.
- [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
> H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
- [reshape2](http://www.jstatsoft.org/v21/i12/)
> Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20.
- [scales](https://CRAN.R-project.org/package=scales)
> Hadley Wickham (2018). scales: Scale Functions for Visualization.
- [pheatmap](https://CRAN.R-project.org/package=pheatmap)
> Raivo Kolde (2018). pheatmap: Pretty Heatmaps.
- [RColorBrewer](https://CRAN.R-project.org/package=RColorBrewer)
> Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes.
- [optparse](https://CRAN.R-project.org/package=optparse)
> Trevor L Davis (2018). optparse: Command Line Option Parser.
## Software packaging/containerisation tools
- [Anaconda](https://anaconda.com)
> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
> Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
================================================
FILE: CODE_OF_CONDUCT.md
================================================
# Code of Conduct at nf-core (v1.0)
## Our Pledge
In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of:
- Age
- Body size
- Familial status
- Gender identity and expression
- Geographical location
- Level of experience
- Nationality and national origins
- Native language
- Physical and neurological ability
- Race or ethnicity
- Religion
- Sexual identity and orientation
- Socioeconomic status
Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance.
## Preamble
> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply.
An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva.
nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals.
We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc.
Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities.
We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC.
Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re
## Our Responsibilities
The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC.
## When are where does this Code of Conduct apply?
Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference:
- Communicating with an official project email address.
- Communicating with community members within the nf-core Slack channel.
- Participating in hackathons organised by nf-core (both online and in-person events).
- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence.
- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc.
- Representing nf-core on social media. This includes both official and personal accounts.
## nf-core cares 😊
nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order):
- Ask for consent before sharing another community member’s personal information (including photographs) on social media.
- Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity.
- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !)
- Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.)
- Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can)
- Focus on what is best for the team and the community. (When in doubt, ask)
- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn.
- Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!)
- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**)
- Take breaks when you feel like you need them.
- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.)
## nf-core frowns on 😕
The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces.
- Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom.
- “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online.
- Spamming or trolling of individuals on social media.
- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention.
- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience.
### Online Trolling
The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately.
All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls.
## Procedures for Reporting CoC violations
If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible.
You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s).
Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course.
All reports will be handled with utmost discretion and confidentially.
## Attribution and Acknowledgements
- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4)
- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition)
- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/)
- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla)
## Changelog
### v1.0 - March 12th, 2021
- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC.
================================================
FILE: LICENSE
================================================
MIT License
Copyright (c) Patel H, Langer B, Espinosa-Carrasco J, Syme R
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
================================================
FILE: README.md
================================================
#  
[](https://nf-co.re/atacseq/results)[](https://doi.org/10.5281/zenodo.2634132)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/atacseq)
[](https://nfcore.slack.com/channels/atacseq)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)
## Introduction
**nfcore/atacseq** is a bioinformatics analysis pipeline used for ATAC-seq data.
The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/atacseq/results).
## Pipeline summary
1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))
3. Choice of multiple aligners
1.([`BWA`](https://sourceforge.net/projects/bio-bwa/files/))
2.([`Chromap`](https://github.com/haowenz/chromap)). **For paired-end reads only working until mapping steps, see [here](https://github.com/nf-core/chipseq/issues/291)**
3.([`Bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
4.([`STAR`](https://github.com/alexdobin/STAR))
4. Mark duplicates ([`picard`](https://broadinstitute.github.io/picard/))
5. Merge alignments from multiple libraries of the same sample ([`picard`](https://broadinstitute.github.io/picard/))
1. Re-mark duplicates ([`picard`](https://broadinstitute.github.io/picard/))
2. Filtering to remove:
- reads mapping to mitochondrial DNA ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
- reads mapping to blacklisted regions ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/), [`BEDTools`](https://github.com/arq5x/bedtools2/))
- reads that are marked as duplicates ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
- reads that are not marked as primary alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
- reads that are unmapped ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
- reads that map to multiple locations ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
- reads containing > 4 mismatches ([`BAMTools`](https://github.com/pezmaster31/bamtools))
- reads that are soft-clipped ([`BAMTools`](https://github.com/pezmaster31/bamtools))
- reads that have an insert size > 2kb ([`BAMTools`](https://github.com/pezmaster31/bamtools); _paired-end only_)
- reads that map to different chromosomes ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
- reads that arent in FR orientation ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
- reads where only one read of the pair fails the above criteria ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)
3. Alignment-level QC and estimation of library complexity ([`picard`](https://broadinstitute.github.io/picard/), [`Preseq`](http://smithlabresearch.org/software/preseq/))
4. Create normalised bigWig files scaled to 1 million mapped reads ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
5. Generate gene-body meta-profile from bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))
6. Calculate genome-wide enrichment (optionally relative to control) ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))
7. Call broad/narrow peaks ([`MACS2`](https://github.com/macs3-project/MACS))
8. Annotate peaks relative to gene features ([`HOMER`](http://homer.ucsd.edu/homer/download.html))
9. Create consensus peakset across all samples and create tabular file to aid in the filtering of the data ([`BEDTools`](https://github.com/arq5x/bedtools2/))
10. Count reads in consensus peaks ([`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))
11. Differential accessibility analysis, PCA and clustering ([`R`](https://www.r-project.org/), [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html))
12. Generate ATAC-seq specific QC html report ([`ataqv`](https://github.com/ParkerLab/ataqv))
6. Merge filtered alignments across replicates ([`picard`](https://broadinstitute.github.io/picard/))
1. Re-mark duplicates ([`picard`](https://broadinstitute.github.io/picard/))
2. Remove duplicate reads ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))
3. Create normalised bigWig files scaled to 1 million mapped reads ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))
4. Call broad/narrow peaks ([`MACS2`](https://github.com/macs3-project/MACS))
5. Annotate peaks relative to gene features ([`HOMER`](http://homer.ucsd.edu/homer/download.html))
6. Create consensus peakset across all samples and create tabular file to aid in the filtering of the data ([`BEDTools`](https://github.com/arq5x/bedtools2/))
7. Count reads in consensus peaks relative to merged library-level alignments ([`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))
8. Differential accessibility analysis, PCA and clustering ([`R`](https://www.r-project.org/), [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html))
7. Create IGV session file containing bigWig tracks, peaks and differential sites for data visualisation ([`IGV`](https://software.broadinstitute.org/software/igv/)).
8. Present QC for raw read, alignment, peak-calling and differential accessibility results ([`ataqv`](https://github.com/ParkerLab/ataqv), [`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))
## Usage
> **Note**
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
> with `-profile test` before running the workflow on actual data.
To run on your data, prepare a tab-separated samplesheet with your input data. Please follow the [documentation on samplesheets](https://nf-co.re/atacseq/usage#samplesheet-input) for more details. An example samplesheet for running the pipeline looks as follows:
```csv
sample,fastq_1,fastq_2,replicate
CONTROL,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,1
CONTROL,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,2
CONTROL,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,3
```
Now, you can run the pipeline using:
```bash
nextflow run nf-core/atacseq --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 --read_length <50|100|150|200> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
See [usage docs](https://nf-co.re/atacseq/usage) for all of the available options when running the pipeline.
> **Warning:**
> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/atacseq/usage) and the [parameter documentation](https://nf-co.re/atacseq/parameters).
## Pipeline output
To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/atacseq/results) tab on the nf-core website pipeline page.
For more details about the output files and reports, please refer to the
[output documentation](https://nf-co.re/atacseq/output).
## Credits
The pipeline was originally written by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and converted to Nextflow DSL2 by Björn Langer ([@bjlang](https://github.com/bjlang)) and Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/) under the umbrella of the [BovReg project](https://www.bovreg.eu/).
Many thanks to others who have helped out and contributed along the way too, including (but not limited to): [@ewels](https://github.com/ewels), [@apeltzer](https://github.com/apeltzer), [@crickbabs](https://github.com/crickbabs), [drewjbeh](https://github.com/drewjbeh), [@houghtos](https://github.com/houghtos), [@jinmingda](https://github.com/jinmingda), [@ktrns](https://github.com/ktrns), [@MaxUlysse](https://github.com/MaxUlysse), [@mashehu](https://github.com/mashehu), [@micans](https://github.com/micans), [@pditommaso](https://github.com/pditommaso) and [@sven1103](https://github.com/sven1103).
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
For further information or help, don't hesitate to get in touch on the [Slack `#atacseq` channel](https://nfcore.slack.com/channels/atacseq) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citations
If you use nf-core/atacseq for your analysis, please cite it using the following doi: [10.5281/zenodo.2634132](https://doi.org/10.5281/zenodo.2634132)
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
You can cite the `nf-core` publication as follows:
> **The nf-core framework for community-curated bioinformatics pipelines.**
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
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12 34432130 34857010 centromeric_repeat 1000 .
12 37989447 38441828 centromeric_repeat 1000 .
12 38531376 38531930 LSU-rRNA_Hsa 1000 .
12 41757383 41757545 Low_mappability_island 1000 .
12 127650407 127651075 LSU-rRNA_Hsa 1000 .
12 132061320 132062046 Low_mappability_island 1000 .
13 56545728 56545925 Low_mappability_island 1000 .
13 110076444 110076782 Low_mappability_island 1000 .
14 18999935 19056900 centromeric_repeat 1000 .
14 32953263 32954381 Low_mappability_island 1000 .
14 84637832 84639038 Low_mappability_island 1000 .
14 90341302 90341516 SSU-rRNA_Hsa 1000 .
15 19999941 20044132 centromeric_repeat 1000 .
16 32493036 32570826 ALR/Alpha 1000 .
16 32590063 32598801 ALR/Alpha 1000 .
16 33237130 33241330 Low_mappability_island 1000 .
16 33864355 34023306 centromeric_repeat 1000 .
16 34180542 34197081 Satellite_repeat 1000 .
16 34530115 34542632 BSR/Beta 1000 .
16 35193580 35285885 centromeric_repeat 1000 .
16 46385718 46456668 Satellite_repeat 1000 .
16 46497639 46500515 Satellite_repeat 1000 .
16 47538629 47539297 LSU-rRNA_Hsa 1000 .
17 19355538 19356096 LSU-rRNA_Hsa 1000 .
17 19502495 19506773 Low_mappability_island 1000 .
17 21905167 21906712 centromeric_repeat 1000 .
17 22018524 22032049 Low_mappability_island 1000 .
17 22221073 22263006 centromeric_repeat 1000 .
17 25263010 25268059 Satellite_repeat 1000 .
17 25415551 25417559 telomeric_repeat 1000 .
17 31149365 31149981 High_Mappability_island 1000 .
17 33478114 33478372 LSU-rRNA_Hsa 1000 .
17 41381502 41382591 High_Mappability_island 1000 .
17 41463538 41464075 High_Mappability_island 1000 .
17 41464478 41465015 snRNA 1000 .
17 41465562 41467288 High_Mappability_island 1000 .
17 51183038 51183763 Low_mappability_island 1000 .
17 55868618 55868752 LSU-rRNA_Hsa 1000 .
17 75158031 75158430 LSU-rRNA_Hsa 1000 .
18 96416 97552 Satellite_repeat 1000 .
18 105658 112233 Satellite_repeat 1000 .
18 2842252 2842356 Low_mappability_island 1000 .
18 15393801 15393992 centromeric_repeat 1000 .
18 18510894 18520356 centromeric_repeat 1000 .
18 44126235 44126593 (CATTC)n 1000 .
18 45379603 45379864 Low_mappability_island 1000 .
18 50319086 50319301 Low_mappability_island 1000 .
18 77772846 77773065 LSU-rRNA_Hsa 1000 .
19 246006 247844 TAR1 1000 .
19 22877614 22877696 SSU-rRNA_Hsa 1000 .
19 23235030 23235504 BSR/Beta 1000 .
19 24182398 24186210 LSU-rRNA_Hsa 1000 .
19 24385474 24633168 centromeric_repeat 1000 .
19 27730611 28262682 centromeric_repeat 1000 .
19 36066445 36066810 LSU-rRNA_Hsa 1000 .
19 36756398 36800948 centromeric_repeat 1000 .
19 37759473 37797722 centromeric_repeat 1000 .
19 44914313 44916340 ACRO1 1000 .
19 44960681 44962681 ACRO1 1000 .
2 739925 740994 Low_mappability_island 1000 .
2 49456729 49457067 Low_mappability_island 1000 .
2 88124390 88124903 Low_mappability_island 1000 .
2 89830421 89880514 Satellite_repeat 1000 .
2 90371401 90394776 Satellite_repeat 1000 .
2 90443001 90545431 Low_mappability_island 1000 .
2 91595080 91616015 Satellite_repeat 1000 .
2 92267428 92326280 centromeric_repeat 1000 .
2 115695017 115695281 LSU-rRNA_Hsa 1000 .
2 117781085 117781300 Low_mappability_island 1000 .
2 132966248 132989300 centromeric_repeat 1000 .
2 132994855 133007983 ALR/Alpha 1000 .
2 133011824 133013298 SSU-rRNA_Hsa 1000 .
2 133036250 133040042 LSU-rRNA_Hsa 1000 .
2 133044095 133045945 ACRO1 1000 .
2 143848503 143848792 Low_mappability_island 1000 .
2 148022736 148022878 Low_mappability_island 1000 .
2 149639207 149639515 Low_mappability_island 1000 .
2 156120500 156120610 Low_mappability_island 1000 .
2 162135000 162139241 Low_mappability_island 1000 .
2 230045426 230045796 LSU-rRNA_Hsa 1000 .
20 26257032 26320267 centromeric_repeat 1000 .
20 29517710 29521147 centromeric_repeat 1000 .
20 29803876 29833334 centromeric_repeat 1000 .
20 55932703 55936114 chrM 1000 .
20 62916702 62918053 telomeric_repeat 1000 .
21 9647205 9648529 Low_mappability_island 1000 .
21 9694896 9704962 centromeric_repeat 1000 .
21 9825451 9827612 High_Mappability_island 1000 .
21 9827612 9845233 Low_mappability_island 1000 .
21 9881895 9882569 TAR1 1000 .
21 10084922 10088004 Satellite_repeat 1000 .
21 10492876 10493049 Low_mappability_island 1000 .
21 10599428 10599915 TAR1 1000 .
21 10697886 10860890 centromeric_repeat 1000 .
21 11186054 11188131 Satellite_repeat 1000 .
21 14338127 14369791 centromeric_repeat 1000 .
21 18800575 18800997 (GAGTG)n 1000 .
21 27228003 27228242 SSU-rRNA_Hsa 1000 .
21 46796081 46796336 Low_mappability_island 1000 .
22 16847814 16862659 Satellite_repeat 1000 .
22 18876789 18884510 Satellite_repeat 1000 .
3 25508897 25509131 Low_mappability_island 1000 .
3 73159606 73161131 snRNA 1000 .
3 75696297 75699304 BSR/Beta 1000 .
3 75717841 75720426 Satellite_repeat 1000 .
3 80995858 81014459 ALR/Alpha 1000 .
3 90311686 90507410 centromeric_repeat 1000 .
3 93504815 93519133 centromeric_repeat 1000 .
3 96335934 96337436 Low_mappability_island 1000 .
3 160665423 160665642 Low_mappability_island 1000 .
3 196625514 196625860 Satellite_repeat 1000 .
3 197825427 197834080 Low_mappability_island 1000 .
4 9987 12694 telomeric_repeat 1000 .
4 12276463 12292424 ALR/Alpha 1000 .
4 12641862 12642305 Low_mappability_island 1000 .
4 21583630 21583719 (GAATG)n 1000 .
4 27732004 27732240 Low_mappability_island 1000 .
4 47774268 47774416 Low_mappability_island 1000 .
4 49085372 49342114 centromeric_repeat 1000 .
4 49488472 49662085 centromeric_repeat 1000 .
4 52659961 52688986 centromeric_repeat 1000 .
4 56194229 56194584 Low_mappability_island 1000 .
4 65473858 65473941 Low_mappability_island 1000 .
4 68264186 68266830 centromeric_repeat 1000 .
4 70296565 70296841 LSU-rRNA_Hsa 1000 .
4 76807083 76807320 LSU-rRNA_Hsa 1000 .
4 78929660 78929920 Low_mappability_island 1000 .
4 156374749 156377226 chrM 1000 .
4 156384860 156387314 Low_mappability_island 1000 .
4 163342479 163342744 Low_mappability_island 1000 .
4 190190746 190203442 Low_mappability_island 1000 .
4 190801869 190802909 Low_mappability_island 1000 .
4 190943802 190943962 Satellite_repeat 1000 .
4 190987268 190990949 Satellite_repeat 1000 .
4 191026302 191044344 telomeric_repeat 1000 .
5 17517177 17600940 Low_mappability_island 1000 .
5 21477365 21497415 Low_mappability_island 1000 .
5 34177882 34197574 Low_mappability_island 1000 .
5 45908253 46411114 centromeric_repeat 1000 .
5 49405493 49554574 centromeric_repeat 1000 .
5 71146650 71146996 LSU-rRNA_Hsa 1000 .
5 79945807 79948223 Low_mappability_island 1000 .
5 93903068 93906726 Low_mappability_island 1000 .
5 97746525 97746679 Low_mappability_island 1000 .
5 99381556 99390873 Low_mappability_island 1000 .
5 105889063 105889263 chrM 1000 .
5 123095972 123097432 chrM 1000 .
5 134258949 134264271 Low_mappability_island 1000 .
5 174541634 174542177 SSU-rRNA_Hsa 1000 .
6 58735349 58739031 centromeric_repeat 1000 .
6 58745955 58780547 centromeric_repeat 1000 .
6 61880095 61944008 centromeric_repeat 1000 .
6 62189892 62206612 ALR/Alpha 1000 .
6 62207809 62230644 ALR/Alpha 1000 .
6 62283966 62284581 Low_mappability_island 1000 .
6 133593944 133594201 LSU-rRNA_Hsa 1000 .
6 137059142 137059326 SSU-rRNA_Hsa 1000 .
6 150665074 150665281 SSU-rRNA_Hsa 1000 .
6 157731310 157735525 Low_mappability_island 1000 .
7 43878355 43878530 TAR1 1000 .
7 45291517 45291740 Low_mappability_island 1000 .
7 56437808 56442977 Low_mappability_island 1000 .
7 57253980 57254183 Low_mappability_island 1000 .
7 57255310 57255444 Low_mappability_island 1000 .
7 57261829 57261998 Low_mappability_island 1000 .
7 57544726 57556913 Satellite_repeat 1000 .
7 57811488 57836990 centromeric_repeat 1000 .
7 57939184 58055539 centromeric_repeat 1000 .
7 61054285 62454680 centromeric_repeat 1000 .
7 64059157 64066183 BSR/Beta 1000 .
7 64951348 64956223 centromeric_repeat 1000 .
7 68201468 68201673 Low_mappability_island 1000 .
7 68527370 68527788 LSU-rRNA_Hsa 1000 .
7 80962907 80963147 SSU-rRNA_Hsa 1000 .
7 100550640 100551321 Low_mappability_island 1000 .
7 142372972 142375638 Low_mappability_island 1000 .
7 145694403 145694561 Low_mappability_island 1000 .
8 155512 157639 TAR1 1000 .
8 21455971 21456306 LSU-rRNA_Hsa 1000 .
8 32868966 32873279 Low_mappability_island 1000 .
8 43092737 43097573 Satellite_repeat 1000 .
8 43399486 43843604 centromeric_repeat 1000 .
8 46838215 47457541 centromeric_repeat 1000 .
8 47739043 47742797 Low_mappability_island 1000 .
8 47750844 47776101 BSR/Beta 1000 .
8 56754955 56755418 LSU-rRNA_Hsa 1000 .
8 69218401 69218922 LSU-rRNA_Hsa 1000 .
8 70602248 70602620 LSU-rRNA_Hsa 1000 .
8 77114154 77114389 Low_mappability_island 1000 .
8 100508010 100508287 Low_mappability_island 1000 .
9 10435 11574 TAR1 1000 .
9 4799734 4800000 SSU-rRNA_Hsa 1000 .
9 33656606 33659249 Low_mappability_island 1000 .
9 42819021 42832395 centromeric_repeat 1000 .
9 44070617 44070871 Low_mappability_island 1000 .
9 44873123 44902307 centromeric_repeat 1000 .
9 45355954 45357644 telomeric_repeat 1000 .
9 45435109 45443517 centromeric_repeat 1000 .
9 66494170 66494805 TAR1 1000 .
9 66767710 66864329 centromeric_repeat 1000 .
9 66970914 67005594 centromeric_repeat 1000 .
9 67315122 67321036 centromeric_repeat 1000 .
9 67789868 67792893 centromeric_repeat 1000 .
9 68410775 68435115 Low_mappability_island 1000 .
9 69677073 69687998 centromeric_repeat 1000 .
9 69689770 69711497 centromeric_repeat 1000 .
9 69947961 70011196 centromeric_repeat 1000 .
9 70076144 70076855 centromeric_repeat 1000 .
9 70318723 70327683 centromeric_repeat 1000 .
9 72653073 72653572 Satellite_repeat 1000 .
9 78790077 78790255 (GAATG)n 1000 .
9 79186574 79187026 LSU-rRNA_Hsa 1000 .
9 141019938 141021783 TAR1 1000 .
MT 1 16569 chrM 1000 .
X 55206111 55206740 Low_mappability_island 1000 .
X 55207753 55208152 Low_mappability_island 1000 .
X 55208300 55208643 Low_mappability_island 1000 .
X 55208980 55209208 Low_mappability_island 1000 .
X 55209655 55210006 Low_mappability_island 1000 .
X 58330488 58330843 centromeric_repeat 1000 .
X 58373806 58373962 centromeric_repeat 1000 .
X 58377680 58377864 centromeric_repeat 1000 .
X 58415350 58416387 centromeric_repeat 1000 .
X 58432411 58432680 centromeric_repeat 1000 .
X 58485887 58486241 centromeric_repeat 1000 .
X 58488898 58494528 centromeric_repeat 1000 .
X 58499466 58504235 centromeric_repeat 1000 .
X 58506076 58528214 centromeric_repeat 1000 .
X 58528184 58536883 centromeric_repeat 1000 .
X 58544061 58582415 centromeric_repeat 1000 .
X 61681834 61919683 centromeric_repeat 1000 .
X 62003205 62041580 centromeric_repeat 1000 .
X 83658929 83659019 Low_mappability_island 1000 .
X 108297348 108297886 LSU-rRNA_Hsa 1000 .
X 114959057 115006437 Low_mappability_island 1000 .
X 125605623 125607351 Low_mappability_island 1000 .
X 125714985 125715338 Low_mappability_island 1000 .
X 125864844 125864980 Low_mappability_island 1000 .
X 125865719 125865874 Low_mappability_island 1000 .
Y 313470 313613 ALR/Alpha 1000 .
Y 3004989 3005175 LSU-rRNA_Hsa 1000 .
Y 4212807 4212910 Low_mappability_island 1000 .
Y 7671817 7694928 BSR/Beta 1000 .
Y 7726064 7730229 BSR/Beta 1000 .
Y 7730734 7731598 BSR/Beta 1000 .
Y 7735811 7752887 BSR/Beta 1000 .
Y 7785067 7806311 BSR/Beta 1000 .
Y 7806856 7814704 BSR/Beta 1000 .
Y 7815230 7820478 BSR/Beta 1000 .
Y 7829937 7832032 BSR/Beta 1000 .
Y 7832744 7848695 BSR/Beta 1000 .
Y 7870343 7873582 BSR/Beta 1000 .
Y 7874115 7874584 BSR/Beta 1000 .
Y 7875409 7885257 BSR/Beta 1000 .
Y 7886545 7894591 BSR/Beta 1000 .
Y 7898927 7916812 BSR/Beta 1000 .
Y 7918790 7921352 BSR/Beta 1000 .
Y 7926344 7936705 BSR/Beta 1000 .
Y 7941130 7947438 BSR/Beta 1000 .
Y 7948790 7964448 BSR/Beta 1000 .
Y 8179010 8181143 BSR/Beta 1000 .
Y 8181757 8213330 BSR/Beta 1000 .
Y 8214629 8215637 BSR/Beta 1000 .
Y 8220421 8230061 BSR/Beta 1000 .
Y 8230686 8231546 BSR/Beta 1000 .
Y 8240772 8265916 BSR/Beta 1000 .
Y 8291535 8292942 BSR/Beta 1000 .
Y 8294002 8295175 BSR/Beta 1000 .
Y 8296944 8321375 BSR/Beta 1000 .
Y 8325813 8325929 BSR/Beta 1000 .
Y 8326678 8333466 BSR/Beta 1000 .
Y 8334027 8342387 BSR/Beta 1000 .
Y 8356544 8369346 BSR/Beta 1000 .
Y 8909560 8909925 TAR1 1000 .
Y 8979478 8979585 Low_mappability_island 1000 .
Y 9072781 9072993 TAR1 1000 .
Y 9908430 9925608 centromeric_repeat 1000 .
Y 9981952 9982126 BSR/Beta 1000 .
Y 10034864 10036712 SSU-rRNA_Hsa 1000 .
Y 10040627 10045657 ALR/Alpha 1000 .
Y 10047773 10052533 ALR/Alpha 1000 .
Y 10053695 10057722 ALR/Alpha 1000 .
Y 10059394 10073694 ALR/Alpha 1000 .
Y 10075082 10075781 ALR/Alpha 1000 .
Y 10080736 10104539 ALR/Alpha 1000 .
Y 13104530 13144368 centromeric_repeat 1000 .
Y 13193966 13196535 Low_mappability_island 1000 .
Y 13252193 13259484 centromeric_repeat 1000 .
Y 13290177 13290667 chrM 1000 .
Y 13445957 13490591 Satellite_repeat 1000 .
Y 13642186 13749784 Satellite_repeat 1000 .
Y 13798522 13870984 Satellite_repeat 1000 .
Y 19691913 19692524 LSU-rRNA_Hsa 1000 .
Y 19764063 19776198 ALR/Alpha 1000 .
Y 19780600 19781704 ALR/Alpha 1000 .
Y 19783669 19796396 ALR/Alpha 1000 .
Y 19800068 19801419 ALR/Alpha 1000 .
Y 19808085 19817100 ALR/Alpha 1000 .
Y 19944298 19944581 TAR1 1000 .
Y 20235195 20235478 TAR1 1000 .
Y 20362679 20371694 ALR/Alpha 1000 .
Y 20378360 20379711 ALR/Alpha 1000 .
Y 20383383 20396110 ALR/Alpha 1000 .
Y 20398075 20399179 ALR/Alpha 1000 .
Y 20403581 20415713 ALR/Alpha 1000 .
Y 20487248 20487859 LSU-rRNA_Hsa 1000 .
Y 23124788 23125577 BSR/Beta 1000 .
Y 23149027 23151205 BSR/Beta 1000 .
Y 23157969 23158245 BSR/Beta 1000 .
Y 23159001 23167737 BSR/Beta 1000 .
Y 23178886 23181770 BSR/Beta 1000 .
Y 23220740 23223625 BSR/Beta 1000 .
Y 23234125 23235822 BSR/Beta 1000 .
Y 23236898 23248080 BSR/Beta 1000 .
Y 23248729 23248851 BSR/Beta 1000 .
Y 23899295 23899388 TAR1 1000 .
Y 23956449 23956628 TAR1 1000 .
Y 24247659 24247700 TAR1 1000 .
Y 24630999 24631040 TAR1 1000 .
Y 24953159 24975657 BSR/Beta 1000 .
Y 24980997 24991235 BSR/Beta 1000 .
Y 25022753 25039185 BSR/Beta 1000 .
Y 25040153 25042421 BSR/Beta 1000 .
Y 25048332 25059258 BSR/Beta 1000 .
Y 25060235 25064798 BSR/Beta 1000 .
Y 25099139 25121882 BSR/Beta 1000 .
Y 25122419 25160800 BSR/Beta 1000 .
Y 25182404 25192372 BSR/Beta 1000 .
Y 25217722 25219409 BSR/Beta 1000 .
Y 25493588 25495275 BSR/Beta 1000 .
Y 26148315 26148450 TAR1 1000 .
Y 26586905 26609405 BSR/Beta 1000 .
Y 26614745 26624983 BSR/Beta 1000 .
Y 26656502 26672934 BSR/Beta 1000 .
Y 26673902 26676170 BSR/Beta 1000 .
Y 26682081 26693007 BSR/Beta 1000 .
Y 26693984 26698547 BSR/Beta 1000 .
Y 26732883 26755623 BSR/Beta 1000 .
Y 26756160 26794538 BSR/Beta 1000 .
Y 26816148 26826116 BSR/Beta 1000 .
Y 26851466 26853153 BSR/Beta 1000 .
Y 27109247 27110934 BSR/Beta 1000 .
Y 27136281 27146249 BSR/Beta 1000 .
Y 27167859 27206241 BSR/Beta 1000 .
Y 27206778 27229502 BSR/Beta 1000 .
Y 27263848 27268411 BSR/Beta 1000 .
Y 27269388 27280315 BSR/Beta 1000 .
Y 27286226 27288494 BSR/Beta 1000 .
Y 27289462 27305895 BSR/Beta 1000 .
Y 27337415 27347656 BSR/Beta 1000 .
Y 27352996 27375497 BSR/Beta 1000 .
Y 27813984 27814119 TAR1 1000 .
Y 28555026 28555353 TAR1 1000 .
Y 28784129 28819695 Satellite_repeat 1000 .
Y 58819367 58917648 (CATTC)n 1000 .
Y 58971913 58997782 (CATTC)n 1000 .
Y 59361267 59362785 TAR1 1000 .
================================================
FILE: assets/blacklists/v1.0/hg19-blacklist.v1.bed
================================================
chr1 564449 570371 High_Mappability_island 1000 .
chr1 724136 727043 Satellite_repeat 1000 .
chr1 825006 825115 BSR/Beta 1000 .
chr1 2583334 2634374 Low_mappability_island 1000 .
chr1 4363064 4363242 (CATTC)n 1000 .
chr1 5725866 5736651 Low_mappability_island 1000 .
chr1 16839923 16841396 Low_mappability_island 1000 .
chr1 38077347 38077423 Low_mappability_island 1000 .
chr1 91852785 91853147 LSU-rRNA_Hsa 1000 .
chr1 104163724 104163860 Low_mappability_island 1000 .
chr1 108112972 108113707 LSU-rRNA_Hsa 1000 .
chr1 121351474 121487059 centromeric_repeat 1000 .
chr1 142535434 142543081 Satellite_repeat 1000 .
chr1 142723256 142723968 Low_mappability_island 1000 .
chr1 142792613 142793303 Low_mappability_island 1000 .
chr1 142835822 142837333 Low_mappability_island 1000 .
chr1 143274490 143284340 centromeric_repeat 1000 .
chr1 145277108 145277572 LSU-rRNA_Hsa 1000 .
chr1 149033183 149035829 Satellite_repeat 1000 .
chr1 156186169 156186712 High_Mappability_island 1000 .
chr1 224199390 224204260 Satellite_repeat 1000 .
chr1 233318467 233318516 (CATTC)n 1000 .
chr1 236260366 236260821 Low_mappability_island 1000 .
chr1 237766308 237766764 LSU-rRNA_Hsa 1000 .
chr1 238105345 238105511 Low_mappability_island 1000 .
chr1 238108025 238108378 Low_mappability_island 1000 .
chr1 238108645 238109697 Low_mappability_island 1000 .
chr10 18841533 18862467 (CATTC)n 1000 .
chr10 20035661 20037171 Low_mappability_island 1000 .
chr10 36722282 36723650 Low_mappability_island 1000 .
chr10 38772277 38819357 Satellite_repeat 1000 .
chr10 38868892 38889025 Satellite_repeat 1000 .
chr10 39076515 39155771 Satellite_repeat 1000 .
chr10 42354835 42548642 centromeric_repeat 1000 .
chr10 42596676 42602082 Satellite_repeat 1000 .
chr10 42596700 42602110 Satellite_repeat 1000 .
chr10 42661264 42667623 Satellite_repeat 1000 .
chr10 42790522 42818398 Satellite_repeat 1000 .
chr10 135498649 135502716 Satellite_repeat 1000 .
chr11 6831669 6831838 ALR/Alpha 1000 .
chr11 10529403 10531969 Low_mappability_island 1000 .
chr11 48671444 48902406 centromeric_repeat 1000 .
chr11 48931242 48964015 centromeric_repeat 1000 .
chr11 50318471 50784078 centromeric_repeat 1000 .
chr11 51090700 51374066 centromeric_repeat 1000 .
chr11 51567242 51594226 centromeric_repeat 1000 .
chr11 54694046 55027975 centromeric_repeat 1000 .
chr11 73221660 73221946 Low_mappability_island 1000 .
chr11 85194913 85195322 LSU-rRNA_Hsa 1000 .
chr11 87524468 87525005 Low_mappability_island 1000 .
chr11 103275584 103281729 Low_mappability_island 1000 .
chr11 122874287 122874443 Low_mappability_island 1000 .
chr12 20704285 20704583 SSU-rRNA_Hsa 1000 .
chr12 34372315 34372825 LSU-rRNA_Hsa 1000 .
chr12 34432130 34857010 centromeric_repeat 1000 .
chr12 37989447 38441828 centromeric_repeat 1000 .
chr12 38531376 38531930 LSU-rRNA_Hsa 1000 .
chr12 41757383 41757545 Low_mappability_island 1000 .
chr12 127650407 127651075 LSU-rRNA_Hsa 1000 .
chr12 132061320 132062046 Low_mappability_island 1000 .
chr13 56545728 56545925 Low_mappability_island 1000 .
chr13 110076444 110076782 Low_mappability_island 1000 .
chr14 18999935 19056900 centromeric_repeat 1000 .
chr14 32953263 32954381 Low_mappability_island 1000 .
chr14 84637832 84639038 Low_mappability_island 1000 .
chr14 90341302 90341516 SSU-rRNA_Hsa 1000 .
chr15 19999941 20044132 centromeric_repeat 1000 .
chr16 32493036 32570826 ALR/Alpha 1000 .
chr16 32590063 32598801 ALR/Alpha 1000 .
chr16 33237130 33241330 Low_mappability_island 1000 .
chr16 33864355 34023306 centromeric_repeat 1000 .
chr16 34180542 34197081 Satellite_repeat 1000 .
chr16 34530115 34542632 BSR/Beta 1000 .
chr16 35193580 35285885 centromeric_repeat 1000 .
chr16 46385718 46456668 Satellite_repeat 1000 .
chr16 46497639 46500515 Satellite_repeat 1000 .
chr16 47538629 47539297 LSU-rRNA_Hsa 1000 .
chr17 19355538 19356096 LSU-rRNA_Hsa 1000 .
chr17 19502495 19506773 Low_mappability_island 1000 .
chr17 21905167 21906712 centromeric_repeat 1000 .
chr17 22018524 22032049 Low_mappability_island 1000 .
chr17 22221073 22263006 centromeric_repeat 1000 .
chr17 25263010 25268059 Satellite_repeat 1000 .
chr17 25415551 25417559 telomeric_repeat 1000 .
chr17 31149365 31149981 High_Mappability_island 1000 .
chr17 33478114 33478372 LSU-rRNA_Hsa 1000 .
chr17 41381502 41382591 High_Mappability_island 1000 .
chr17 41463538 41464075 High_Mappability_island 1000 .
chr17 41464478 41465015 snRNA 1000 .
chr17 41465562 41467288 High_Mappability_island 1000 .
chr17 51183038 51183763 Low_mappability_island 1000 .
chr17 55868618 55868752 LSU-rRNA_Hsa 1000 .
chr17 75158031 75158430 LSU-rRNA_Hsa 1000 .
chr18 96416 97552 Satellite_repeat 1000 .
chr18 105658 112233 Satellite_repeat 1000 .
chr18 2842252 2842356 Low_mappability_island 1000 .
chr18 15393801 15393992 centromeric_repeat 1000 .
chr18 18510894 18520356 centromeric_repeat 1000 .
chr18 44126235 44126593 (CATTC)n 1000 .
chr18 45379603 45379864 Low_mappability_island 1000 .
chr18 50319086 50319301 Low_mappability_island 1000 .
chr18 77772846 77773065 LSU-rRNA_Hsa 1000 .
chr19 246006 247844 TAR1 1000 .
chr19 22877614 22877696 SSU-rRNA_Hsa 1000 .
chr19 23235030 23235504 BSR/Beta 1000 .
chr19 24182398 24186210 LSU-rRNA_Hsa 1000 .
chr19 24385474 24633168 centromeric_repeat 1000 .
chr19 27730611 28262682 centromeric_repeat 1000 .
chr19 36066445 36066810 LSU-rRNA_Hsa 1000 .
chr19 36756398 36800948 centromeric_repeat 1000 .
chr19 37759473 37797722 centromeric_repeat 1000 .
chr19 44914313 44916340 ACRO1 1000 .
chr19 44960681 44962681 ACRO1 1000 .
chr2 739925 740994 Low_mappability_island 1000 .
chr2 49456729 49457067 Low_mappability_island 1000 .
chr2 88124390 88124903 Low_mappability_island 1000 .
chr2 89830421 89880514 Satellite_repeat 1000 .
chr2 90371401 90394776 Satellite_repeat 1000 .
chr2 90443001 90545431 Low_mappability_island 1000 .
chr2 91595080 91616015 Satellite_repeat 1000 .
chr2 92267428 92326280 centromeric_repeat 1000 .
chr2 115695017 115695281 LSU-rRNA_Hsa 1000 .
chr2 117781085 117781300 Low_mappability_island 1000 .
chr2 132966248 132989300 centromeric_repeat 1000 .
chr2 132994855 133007983 ALR/Alpha 1000 .
chr2 133011824 133013298 SSU-rRNA_Hsa 1000 .
chr2 133036250 133040042 LSU-rRNA_Hsa 1000 .
chr2 133044095 133045945 ACRO1 1000 .
chr2 143848503 143848792 Low_mappability_island 1000 .
chr2 148022736 148022878 Low_mappability_island 1000 .
chr2 149639207 149639515 Low_mappability_island 1000 .
chr2 156120500 156120610 Low_mappability_island 1000 .
chr2 162135000 162139241 Low_mappability_island 1000 .
chr2 230045426 230045796 LSU-rRNA_Hsa 1000 .
chr20 26257032 26320267 centromeric_repeat 1000 .
chr20 29517710 29521147 centromeric_repeat 1000 .
chr20 29803876 29833334 centromeric_repeat 1000 .
chr20 55932703 55936114 chrM 1000 .
chr20 62916702 62918053 telomeric_repeat 1000 .
chr21 9647205 9648529 Low_mappability_island 1000 .
chr21 9694896 9704962 centromeric_repeat 1000 .
chr21 9825451 9827612 High_Mappability_island 1000 .
chr21 9827612 9845233 Low_mappability_island 1000 .
chr21 9881895 9882569 TAR1 1000 .
chr21 10084922 10088004 Satellite_repeat 1000 .
chr21 10492876 10493049 Low_mappability_island 1000 .
chr21 10599428 10599915 TAR1 1000 .
chr21 10697886 10860890 centromeric_repeat 1000 .
chr21 11186054 11188131 Satellite_repeat 1000 .
chr21 14338127 14369791 centromeric_repeat 1000 .
chr21 18800575 18800997 (GAGTG)n 1000 .
chr21 27228003 27228242 SSU-rRNA_Hsa 1000 .
chr21 46796081 46796336 Low_mappability_island 1000 .
chr22 16847814 16862659 Satellite_repeat 1000 .
chr22 18876789 18884510 Satellite_repeat 1000 .
chr3 25508897 25509131 Low_mappability_island 1000 .
chr3 73159606 73161131 snRNA 1000 .
chr3 75696297 75699304 BSR/Beta 1000 .
chr3 75717841 75720426 Satellite_repeat 1000 .
chr3 80995858 81014459 ALR/Alpha 1000 .
chr3 90311686 90507410 centromeric_repeat 1000 .
chr3 93504815 93519133 centromeric_repeat 1000 .
chr3 96335934 96337436 Low_mappability_island 1000 .
chr3 160665423 160665642 Low_mappability_island 1000 .
chr3 196625514 196625860 Satellite_repeat 1000 .
chr3 197825427 197834080 Low_mappability_island 1000 .
chr4 9987 12694 telomeric_repeat 1000 .
chr4 12276463 12292424 ALR/Alpha 1000 .
chr4 12641862 12642305 Low_mappability_island 1000 .
chr4 21583630 21583719 (GAATG)n 1000 .
chr4 27732004 27732240 Low_mappability_island 1000 .
chr4 47774268 47774416 Low_mappability_island 1000 .
chr4 49085372 49342114 centromeric_repeat 1000 .
chr4 49488472 49662085 centromeric_repeat 1000 .
chr4 52659961 52688986 centromeric_repeat 1000 .
chr4 56194229 56194584 Low_mappability_island 1000 .
chr4 65473858 65473941 Low_mappability_island 1000 .
chr4 68264186 68266830 centromeric_repeat 1000 .
chr4 70296565 70296841 LSU-rRNA_Hsa 1000 .
chr4 76807083 76807320 LSU-rRNA_Hsa 1000 .
chr4 78929660 78929920 Low_mappability_island 1000 .
chr4 156374749 156377226 chrM 1000 .
chr4 156384860 156387314 Low_mappability_island 1000 .
chr4 163342479 163342744 Low_mappability_island 1000 .
chr4 190190746 190203442 Low_mappability_island 1000 .
chr4 190801869 190802909 Low_mappability_island 1000 .
chr4 190943802 190943962 Satellite_repeat 1000 .
chr4 190987268 190990949 Satellite_repeat 1000 .
chr4 191026302 191044344 telomeric_repeat 1000 .
chr5 17517177 17600940 Low_mappability_island 1000 .
chr5 21477365 21497415 Low_mappability_island 1000 .
chr5 34177882 34197574 Low_mappability_island 1000 .
chr5 45908253 46411114 centromeric_repeat 1000 .
chr5 49405493 49554574 centromeric_repeat 1000 .
chr5 71146650 71146996 LSU-rRNA_Hsa 1000 .
chr5 79945807 79948223 Low_mappability_island 1000 .
chr5 93903068 93906726 Low_mappability_island 1000 .
chr5 97746525 97746679 Low_mappability_island 1000 .
chr5 99381556 99390873 Low_mappability_island 1000 .
chr5 105889063 105889263 chrM 1000 .
chr5 123095972 123097432 chrM 1000 .
chr5 134258949 134264271 Low_mappability_island 1000 .
chr5 174541634 174542177 SSU-rRNA_Hsa 1000 .
chr6 58735349 58739031 centromeric_repeat 1000 .
chr6 58745955 58780547 centromeric_repeat 1000 .
chr6 61880095 61944008 centromeric_repeat 1000 .
chr6 62189892 62206612 ALR/Alpha 1000 .
chr6 62207809 62230644 ALR/Alpha 1000 .
chr6 62283966 62284581 Low_mappability_island 1000 .
chr6 133593944 133594201 LSU-rRNA_Hsa 1000 .
chr6 137059142 137059326 SSU-rRNA_Hsa 1000 .
chr6 150665074 150665281 SSU-rRNA_Hsa 1000 .
chr6 157731310 157735525 Low_mappability_island 1000 .
chr7 43878355 43878530 TAR1 1000 .
chr7 45291517 45291740 Low_mappability_island 1000 .
chr7 56437808 56442977 Low_mappability_island 1000 .
chr7 57253980 57254183 Low_mappability_island 1000 .
chr7 57255310 57255444 Low_mappability_island 1000 .
chr7 57261829 57261998 Low_mappability_island 1000 .
chr7 57544726 57556913 Satellite_repeat 1000 .
chr7 57811488 57836990 centromeric_repeat 1000 .
chr7 57939184 58055539 centromeric_repeat 1000 .
chr7 61054285 62454680 centromeric_repeat 1000 .
chr7 64059157 64066183 BSR/Beta 1000 .
chr7 64951348 64956223 centromeric_repeat 1000 .
chr7 68201468 68201673 Low_mappability_island 1000 .
chr7 68527370 68527788 LSU-rRNA_Hsa 1000 .
chr7 80962907 80963147 SSU-rRNA_Hsa 1000 .
chr7 100550640 100551321 Low_mappability_island 1000 .
chr7 142372972 142375638 Low_mappability_island 1000 .
chr7 145694403 145694561 Low_mappability_island 1000 .
chr8 155512 157639 TAR1 1000 .
chr8 21455971 21456306 LSU-rRNA_Hsa 1000 .
chr8 32868966 32873279 Low_mappability_island 1000 .
chr8 43092737 43097573 Satellite_repeat 1000 .
chr8 43399486 43843604 centromeric_repeat 1000 .
chr8 46838215 47457541 centromeric_repeat 1000 .
chr8 47739043 47742797 Low_mappability_island 1000 .
chr8 47750844 47776101 BSR/Beta 1000 .
chr8 56754955 56755418 LSU-rRNA_Hsa 1000 .
chr8 69218401 69218922 LSU-rRNA_Hsa 1000 .
chr8 70602248 70602620 LSU-rRNA_Hsa 1000 .
chr8 77114154 77114389 Low_mappability_island 1000 .
chr8 100508010 100508287 Low_mappability_island 1000 .
chr9 10435 11574 TAR1 1000 .
chr9 4799734 4800000 SSU-rRNA_Hsa 1000 .
chr9 33656606 33659249 Low_mappability_island 1000 .
chr9 42819021 42832395 centromeric_repeat 1000 .
chr9 44070617 44070871 Low_mappability_island 1000 .
chr9 44873123 44902307 centromeric_repeat 1000 .
chr9 45355954 45357644 telomeric_repeat 1000 .
chr9 45435109 45443517 centromeric_repeat 1000 .
chr9 66494170 66494805 TAR1 1000 .
chr9 66767710 66864329 centromeric_repeat 1000 .
chr9 66970914 67005594 centromeric_repeat 1000 .
chr9 67315122 67321036 centromeric_repeat 1000 .
chr9 67789868 67792893 centromeric_repeat 1000 .
chr9 68410775 68435115 Low_mappability_island 1000 .
chr9 69677073 69687998 centromeric_repeat 1000 .
chr9 69689770 69711497 centromeric_repeat 1000 .
chr9 69947961 70011196 centromeric_repeat 1000 .
chr9 70076144 70076855 centromeric_repeat 1000 .
chr9 70318723 70327683 centromeric_repeat 1000 .
chr9 72653073 72653572 Satellite_repeat 1000 .
chr9 78790077 78790255 (GAATG)n 1000 .
chr9 79186574 79187026 LSU-rRNA_Hsa 1000 .
chr9 141019938 141021783 TAR1 1000 .
chrM 1 16571 chrM 1000 .
chrX 55206111 55206740 Low_mappability_island 1000 .
chrX 55207753 55208152 Low_mappability_island 1000 .
chrX 55208300 55208643 Low_mappability_island 1000 .
chrX 55208980 55209208 Low_mappability_island 1000 .
chrX 55209655 55210006 Low_mappability_island 1000 .
chrX 58330488 58330843 centromeric_repeat 1000 .
chrX 58373806 58373962 centromeric_repeat 1000 .
chrX 58377680 58377864 centromeric_repeat 1000 .
chrX 58415350 58416387 centromeric_repeat 1000 .
chrX 58432411 58432680 centromeric_repeat 1000 .
chrX 58485887 58486241 centromeric_repeat 1000 .
chrX 58488898 58494528 centromeric_repeat 1000 .
chrX 58499466 58504235 centromeric_repeat 1000 .
chrX 58506076 58528214 centromeric_repeat 1000 .
chrX 58528184 58536883 centromeric_repeat 1000 .
chrX 58544061 58582415 centromeric_repeat 1000 .
chrX 61681834 61919683 centromeric_repeat 1000 .
chrX 62003205 62041580 centromeric_repeat 1000 .
chrX 83658929 83659019 Low_mappability_island 1000 .
chrX 108297348 108297886 LSU-rRNA_Hsa 1000 .
chrX 114959057 115006437 Low_mappability_island 1000 .
chrX 125605623 125607351 Low_mappability_island 1000 .
chrX 125714985 125715338 Low_mappability_island 1000 .
chrX 125864844 125864980 Low_mappability_island 1000 .
chrX 125865719 125865874 Low_mappability_island 1000 .
chrY 313470 313613 ALR/Alpha 1000 .
chrY 3004989 3005175 LSU-rRNA_Hsa 1000 .
chrY 4212807 4212910 Low_mappability_island 1000 .
chrY 7671817 7694928 BSR/Beta 1000 .
chrY 7726064 7730229 BSR/Beta 1000 .
chrY 7730734 7731598 BSR/Beta 1000 .
chrY 7735811 7752887 BSR/Beta 1000 .
chrY 7785067 7806311 BSR/Beta 1000 .
chrY 7806856 7814704 BSR/Beta 1000 .
chrY 7815230 7820478 BSR/Beta 1000 .
chrY 7829937 7832032 BSR/Beta 1000 .
chrY 7832744 7848695 BSR/Beta 1000 .
chrY 7870343 7873582 BSR/Beta 1000 .
chrY 7874115 7874584 BSR/Beta 1000 .
chrY 7875409 7885257 BSR/Beta 1000 .
chrY 7886545 7894591 BSR/Beta 1000 .
chrY 7898927 7916812 BSR/Beta 1000 .
chrY 7918790 7921352 BSR/Beta 1000 .
chrY 7926344 7936705 BSR/Beta 1000 .
chrY 7941130 7947438 BSR/Beta 1000 .
chrY 7948790 7964448 BSR/Beta 1000 .
chrY 8179010 8181143 BSR/Beta 1000 .
chrY 8181757 8213330 BSR/Beta 1000 .
chrY 8214629 8215637 BSR/Beta 1000 .
chrY 8220421 8230061 BSR/Beta 1000 .
chrY 8230686 8231546 BSR/Beta 1000 .
chrY 8240772 8265916 BSR/Beta 1000 .
chrY 8291535 8292942 BSR/Beta 1000 .
chrY 8294002 8295175 BSR/Beta 1000 .
chrY 8296944 8321375 BSR/Beta 1000 .
chrY 8325813 8325929 BSR/Beta 1000 .
chrY 8326678 8333466 BSR/Beta 1000 .
chrY 8334027 8342387 BSR/Beta 1000 .
chrY 8356544 8369346 BSR/Beta 1000 .
chrY 8909560 8909925 TAR1 1000 .
chrY 8979478 8979585 Low_mappability_island 1000 .
chrY 9072781 9072993 TAR1 1000 .
chrY 9908430 9925608 centromeric_repeat 1000 .
chrY 9981952 9982126 BSR/Beta 1000 .
chrY 10034864 10036712 SSU-rRNA_Hsa 1000 .
chrY 10040627 10045657 ALR/Alpha 1000 .
chrY 10047773 10052533 ALR/Alpha 1000 .
chrY 10053695 10057722 ALR/Alpha 1000 .
chrY 10059394 10073694 ALR/Alpha 1000 .
chrY 10075082 10075781 ALR/Alpha 1000 .
chrY 10080736 10104539 ALR/Alpha 1000 .
chrY 13104530 13144368 centromeric_repeat 1000 .
chrY 13193966 13196535 Low_mappability_island 1000 .
chrY 13252193 13259484 centromeric_repeat 1000 .
chrY 13290177 13290667 chrM 1000 .
chrY 13445957 13490591 Satellite_repeat 1000 .
chrY 13642186 13749784 Satellite_repeat 1000 .
chrY 13798522 13870984 Satellite_repeat 1000 .
chrY 19691913 19692524 LSU-rRNA_Hsa 1000 .
chrY 19764063 19776198 ALR/Alpha 1000 .
chrY 19780600 19781704 ALR/Alpha 1000 .
chrY 19783669 19796396 ALR/Alpha 1000 .
chrY 19800068 19801419 ALR/Alpha 1000 .
chrY 19808085 19817100 ALR/Alpha 1000 .
chrY 19944298 19944581 TAR1 1000 .
chrY 20235195 20235478 TAR1 1000 .
chrY 20362679 20371694 ALR/Alpha 1000 .
chrY 20378360 20379711 ALR/Alpha 1000 .
chrY 20383383 20396110 ALR/Alpha 1000 .
chrY 20398075 20399179 ALR/Alpha 1000 .
chrY 20403581 20415713 ALR/Alpha 1000 .
chrY 20487248 20487859 LSU-rRNA_Hsa 1000 .
chrY 23124788 23125577 BSR/Beta 1000 .
chrY 23149027 23151205 BSR/Beta 1000 .
chrY 23157969 23158245 BSR/Beta 1000 .
chrY 23159001 23167737 BSR/Beta 1000 .
chrY 23178886 23181770 BSR/Beta 1000 .
chrY 23220740 23223625 BSR/Beta 1000 .
chrY 23234125 23235822 BSR/Beta 1000 .
chrY 23236898 23248080 BSR/Beta 1000 .
chrY 23248729 23248851 BSR/Beta 1000 .
chrY 23899295 23899388 TAR1 1000 .
chrY 23956449 23956628 TAR1 1000 .
chrY 24247659 24247700 TAR1 1000 .
chrY 24630999 24631040 TAR1 1000 .
chrY 24953159 24975657 BSR/Beta 1000 .
chrY 24980997 24991235 BSR/Beta 1000 .
chrY 25022753 25039185 BSR/Beta 1000 .
chrY 25040153 25042421 BSR/Beta 1000 .
chrY 25048332 25059258 BSR/Beta 1000 .
chrY 25060235 25064798 BSR/Beta 1000 .
chrY 25099139 25121882 BSR/Beta 1000 .
chrY 25122419 25160800 BSR/Beta 1000 .
chrY 25182404 25192372 BSR/Beta 1000 .
chrY 25217722 25219409 BSR/Beta 1000 .
chrY 25493588 25495275 BSR/Beta 1000 .
chrY 26148315 26148450 TAR1 1000 .
chrY 26586905 26609405 BSR/Beta 1000 .
chrY 26614745 26624983 BSR/Beta 1000 .
chrY 26656502 26672934 BSR/Beta 1000 .
chrY 26673902 26676170 BSR/Beta 1000 .
chrY 26682081 26693007 BSR/Beta 1000 .
chrY 26693984 26698547 BSR/Beta 1000 .
chrY 26732883 26755623 BSR/Beta 1000 .
chrY 26756160 26794538 BSR/Beta 1000 .
chrY 26816148 26826116 BSR/Beta 1000 .
chrY 26851466 26853153 BSR/Beta 1000 .
chrY 27109247 27110934 BSR/Beta 1000 .
chrY 27136281 27146249 BSR/Beta 1000 .
chrY 27167859 27206241 BSR/Beta 1000 .
chrY 27206778 27229502 BSR/Beta 1000 .
chrY 27263848 27268411 BSR/Beta 1000 .
chrY 27269388 27280315 BSR/Beta 1000 .
chrY 27286226 27288494 BSR/Beta 1000 .
chrY 27289462 27305895 BSR/Beta 1000 .
chrY 27337415 27347656 BSR/Beta 1000 .
chrY 27352996 27375497 BSR/Beta 1000 .
chrY 27813984 27814119 TAR1 1000 .
chrY 28555026 28555353 TAR1 1000 .
chrY 28784129 28819695 Satellite_repeat 1000 .
chrY 58819367 58917648 (CATTC)n 1000 .
chrY 58971913 58997782 (CATTC)n 1000 .
chrY 59361267 59362785 TAR1 1000 .
================================================
FILE: assets/blacklists/v2.0/GRCm38-blacklist.v2.bed
================================================
10 0 3135400 High Signal Region
10 3218900 3276600 Low Mappability
10 3576900 3627700 Low Mappability
10 4191100 4197600 Low Mappability
10 4613500 4615400 High Signal Region
10 4761300 4763900 High Signal Region
10 5080800 5096600 Low Mappability
10 5580100 5586600 Low Mappability
10 6281200 6286700 High Signal Region
10 6740200 6742100 High Signal Region
10 7396300 7429800 High Signal Region
10 7633600 7636600 Low Mappability
10 7889700 7897500 High Signal Region
10 8144900 8153000 High Signal Region
10 8264000 8269200 High Signal Region
10 8382400 8404400 High Signal Region
10 8599200 8606400 Low Mappability
10 10012200 10033400 High Signal Region
10 10566900 10593500 High Signal Region
10 11218400 11224800 Low Mappability
10 11351800 11406300 Low Mappability
10 11491200 11493100 High Signal Region
10 11612300 11642500 High Signal Region
10 11692500 11701300 Low Mappability
10 12266500 12273000 High Signal Region
10 12385800 12396000 High Signal Region
10 13401200 13403100 High Signal Region
10 14559900 14577100 High Signal Region
10 14646300 14664500 Low Mappability
10 14923800 14928300 High Signal Region
10 15047600 15083100 High Signal Region
10 15528600 15534200 High Signal Region
10 15567000 15641800 High Signal Region
10 16967500 16971600 High Signal Region
10 17499600 17501700 High Signal Region
10 18555500 18558100 High Signal Region
10 19427600 19429100 High Signal Region
10 19538800 19546100 Low Mappability
10 19772200 19801600 High Signal Region
10 20458900 20460800 High Signal Region
10 21208600 21216600 Low Mappability
10 21278500 21313500 High Signal Region
10 21642200 21649600 Low Mappability
10 21727800 21736400 Low Mappability
10 22031300 22063500 High Signal Region
10 22127200 22164500 High Signal Region
10 22186700 22290500 High Signal Region
10 22369100 22472300 High Signal Region
10 22683100 22690600 Low Mappability
10 22935900 22941800 High Signal Region
10 24687500 24691700 Low Mappability
10 25091400 25106900 Low Mappability
10 25622900 25629400 Low Mappability
10 25968400 25973400 Low Mappability
10 26641500 26662800 Low Mappability
10 27403200 27407600 High Signal Region
10 27904000 27909500 High Signal Region
10 28908500 28940600 High Signal Region
10 29243900 29249600 High Signal Region
10 29924300 29930700 Low Mappability
10 29954000 29971900 High Signal Region
10 30553000 30577100 High Signal Region
10 31054900 31095900 Low Mappability
10 31406500 31411100 High Signal Region
10 31750000 31757100 Low Mappability
10 31878400 31885800 High Signal Region
10 31980100 32000400 Low Mappability
10 32039700 32045000 High Signal Region
10 32176100 32182400 High Signal Region
10 32499200 32529900 High Signal Region
10 32816400 32857200 High Signal Region
10 33315300 33319800 High Signal Region
10 33492300 33508900 High Signal Region
10 33886600 33901100 Low Mappability
10 34739400 34749100 Low Mappability
10 35669300 35725500 High Signal Region
10 36130200 36135500 High Signal Region
10 36160700 36166700 High Signal Region
10 36594500 36597500 Low Mappability
10 36942200 36948800 Low Mappability
10 37186500 37189300 High Signal Region
10 37799700 37821400 High Signal Region
10 37964600 37970100 High Signal Region
10 38590100 38606100 High Signal Region
10 38637900 38644200 High Signal Region
10 38729400 38782700 High Signal Region
10 38933500 38956500 High Signal Region
10 39126700 39129400 High Signal Region
10 39760700 39764700 High Signal Region
10 41185700 41195800 High Signal Region
10 41840500 41859100 Low Mappability
10 43769400 43773800 High Signal Region
10 44206300 44254100 High Signal Region
10 45515000 45588000 Low Mappability
10 45624800 45628400 High Signal Region
10 46136500 46139300 High Signal Region
10 46468300 46472100 High Signal Region
10 46500500 46538800 High Signal Region
10 46789300 46812500 High Signal Region
10 46966700 47009000 High Signal Region
10 47048600 47074700 Low Mappability
10 47663600 47683500 High Signal Region
10 47743600 47758500 High Signal Region
10 47875400 47881600 High Signal Region
10 48032400 48058800 High Signal Region
10 48677400 48682800 High Signal Region
10 49823500 49842200 High Signal Region
10 50029200 50035300 High Signal Region
10 50109900 50115500 High Signal Region
10 50178500 50184800 High Signal Region
10 50253700 50296500 High Signal Region
10 50333400 50335300 High Signal Region
10 50524000 50553900 High Signal Region
10 51126200 51132900 High Signal Region
10 51436800 51448000 High Signal Region
10 51470300 51474900 High Signal Region
10 51882900 51888000 Low Mappability
10 52052600 52059000 Low Mappability
10 52089600 52148500 High Signal Region
10 52522600 52599800 High Signal Region
10 53073900 53081100 High Signal Region
10 53569600 53576000 Low Mappability
10 54216200 54222900 High Signal Region
10 54588800 54619900 Low Mappability
10 55080400 55090500 High Signal Region
10 55654500 55659600 High Signal Region
10 55715600 55751000 High Signal Region
10 55841700 55847900 High Signal Region
10 56250200 56293900 High Signal Region
10 56701000 56728000 High Signal Region
10 56894100 56897300 High Signal Region
10 57099200 57153200 High Signal Region
10 57239100 57245400 High Signal Region
10 57326900 57333900 High Signal Region
10 57434000 57456500 High Signal Region
10 57678600 57684900 High Signal Region
10 57862800 58240900 High Signal Region
10 58566200 58570900 High Signal Region
10 59381400 59396800 Low Mappability
10 59850500 59922300 Low Mappability
10 60444900 60446800 High Signal Region
10 60546600 60553100 Low Mappability
10 61373100 61375000 High Signal Region
10 63103900 63111200 Low Mappability
10 63508800 63519000 High Signal Region
10 63833800 63835000 High Signal Region
10 64418600 64420000 High Signal Region
10 65166300 65172600 High Signal Region
10 65450400 65477700 High Signal Region
10 65638900 65670200 High Signal Region
10 65938900 65956300 Low Mappability
10 66422900 66431000 High Signal Region
10 66662400 66678300 High Signal Region
10 69030100 69065800 High Signal Region
10 70657500 70668500 High Signal Region
10 70785400 70798600 Low Mappability
10 71012700 71019200 Low Mappability
10 71111600 71114200 Low Mappability
10 71510600 71637800 High Signal Region
10 71691300 71698600 Low Mappability
10 72292400 72314300 High Signal Region
10 72359200 72360700 High Signal Region
10 72493500 72499200 High Signal Region
10 72590700 72591900 High Signal Region
10 72690900 72709500 High Signal Region
10 73378200 73380100 High Signal Region
10 73576400 73601900 High Signal Region
10 74433300 74439500 High Signal Region
10 74655700 74672200 High Signal Region
10 74715300 74746600 High Signal Region
10 74857500 74888000 High Signal Region
10 76835100 76852400 High Signal Region
10 77950600 77979500 Low Mappability
10 78008300 78028800 Low Mappability
10 78637000 78696000 High Signal Region
10 78731500 78735800 High Signal Region
10 78803500 78823100 Low Mappability
10 79207800 79259400 High Signal Region
10 79314000 79354000 Low Mappability
10 80102300 80116000 High Signal Region
10 80928600 80996300 Low Mappability
10 81167600 81199400 High Signal Region
10 81600900 81997900 High Signal Region
10 82517500 82538800 High Signal Region
10 82571100 82575200 High Signal Region
10 82939800 82956300 High Signal Region
10 83386600 83392400 Low Mappability
10 83670800 83678100 Low Mappability
10 83768200 83792700 Low Mappability
10 84155900 84180800 Low Mappability
10 84436900 84473700 Low Mappability
10 84744500 84750100 Low Mappability
10 85413200 85419700 Low Mappability
10 85696600 85732800 High Signal Region
10 85840200 85872500 High Signal Region
10 86561700 86565700 High Signal Region
10 88628700 88658500 Low Mappability
10 88963900 88968200 Low Mappability
10 89398700 89400100 High Signal Region
10 89949700 89964500 High Signal Region
10 90249000 90255300 High Signal Region
10 90324500 90329800 Low Mappability
10 90471200 90474200 Low Mappability
10 91252200 91256900 High Signal Region
10 91928900 91944500 High Signal Region
10 92909200 92915800 High Signal Region
10 94362500 94369300 Low Mappability
10 94591500 94610000 High Signal Region
10 94871200 94873100 High Signal Region
10 96068700 96078800 High Signal Region
10 96157200 96162600 Low Mappability
10 96192400 96199800 Low Mappability
10 97320500 97329700 High Signal Region
10 97525500 97534200 Low Mappability
10 97755000 97761200 High Signal Region
10 97896600 97920300 High Signal Region
10 98337800 98343700 High Signal Region
10 98433100 98444100 High Signal Region
10 100310500 100395900 High Signal Region
10 102667700 102669600 High Signal Region
10 102859800 102861500 High Signal Region
10 103500200 103519100 High Signal Region
10 103547000 103548600 High Signal Region
10 103569600 103575200 High Signal Region
10 103600400 103684400 High Signal Region
10 103936700 103942500 High Signal Region
10 104380700 104382300 High Signal Region
10 104493600 104499800 High Signal Region
10 104539700 104562500 Low Mappability
10 104748100 104771500 High Signal Region
10 104819400 104862500 Low Mappability
10 104966900 105001700 Low Mappability
10 105177000 105181900 Low Mappability
10 105672500 105678000 Low Mappability
10 106166900 106235700 High Signal Region
10 106382800 106403000 High Signal Region
10 106427100 106453600 High Signal Region
10 106529600 106535200 Low Mappability
10 107125500 107136900 Low Mappability
10 107551800 107560700 High Signal Region
10 107845300 107863900 High Signal Region
10 107978900 108006700 Low Mappability
10 109212600 109216800 High Signal Region
10 109315100 109322400 Low Mappability
10 109941600 109948000 High Signal Region
10 110104900 110111300 Low Mappability
10 110504500 110516000 High Signal Region
10 110667700 110700900 Low Mappability
10 111217500 111219000 High Signal Region
10 112013700 112021700 High Signal Region
10 112053500 112058400 Low Mappability
10 112540600 112542100 High Signal Region
10 112587000 112611100 High Signal Region
10 112682400 112722100 Low Mappability
10 113722600 113729800 Low Mappability
10 114167300 114174900 High Signal Region
10 114736400 114738300 High Signal Region
10 114860600 114866900 High Signal Region
10 115641300 115643100 High Signal Region
10 116606200 116613400 Low Mappability
10 116762000 116764200 High Signal Region
10 116878000 116879900 High Signal Region
10 117476200 117491000 High Signal Region
10 118014300 118033200 High Signal Region
10 118054000 118076600 High Signal Region
10 118199900 118279700 Low Mappability
10 118910200 118917100 High Signal Region
10 118937400 118953000 Low Mappability
10 119698800 119701600 Low Mappability
10 120974800 120977500 High Signal Region
10 121136000 121143400 Low Mappability
10 121164700 121169300 Low Mappability
10 121566100 121580200 High Signal Region
10 121707800 121713500 High Signal Region
10 121762300 121769400 High Signal Region
10 122141100 122166000 High Signal Region
10 122346900 122371300 Low Mappability
10 122632400 122638000 High Signal Region
10 122832900 122839300 High Signal Region
10 123792900 123797100 High Signal Region
10 124412900 124433300 High Signal Region
10 124576300 124583500 Low Mappability
10 124605700 124611000 Low Mappability
10 124680500 124686200 Low Mappability
10 124760500 124788800 High Signal Region
10 125819500 125825700 High Signal Region
10 125869000 125871400 High Signal Region
10 126262200 126291600 Low Mappability
10 127779500 127797900 High Signal Region
10 129189500 129217200 High Signal Region
10 129388700 129419600 Low Mappability
10 129443000 129454800 High Signal Region
10 129734500 129736400 High Signal Region
10 129925300 129940600 Low Mappability
10 130039500 130052900 High Signal Region
10 130396900 130408000 High Signal Region
10 130542000 130694900 High Signal Region
11 0 3201000 High Signal Region
11 5167600 5182600 High Signal Region
11 5361500 5365400 Low Mappability
11 5552700 5558200 Low Mappability
11 6141300 6148700 Low Mappability
11 7489400 7492300 High Signal Region
11 7752300 7774500 Low Mappability
11 8058600 8083100 Low Mappability
11 8354900 8370700 High Signal Region
11 8907200 8936100 Low Mappability
11 9707900 9715100 Low Mappability
11 9807600 9814200 Low Mappability
11 10252000 10266800 High Signal Region
11 10760200 10770800 Low Mappability
11 11287200 11295100 High Signal Region
11 12129400 12163100 High Signal Region
11 12507200 12512700 Low Mappability
11 12561900 12569100 Low Mappability
11 12750500 12802700 High Signal Region
11 12856200 12863700 High Signal Region
11 12953900 12960700 Low Mappability
11 14896500 14922100 High Signal Region
11 15227600 15235000 Low Mappability
11 16022400 16029000 High Signal Region
11 16326500 16331700 High Signal Region
11 16418200 16419600 High Signal Region
11 16567100 16573100 High Signal Region
11 17401400 17407800 High Signal Region
11 18330900 18342700 High Signal Region
11 18773800 18780100 High Signal Region
11 19566100 19570600 Low Mappability
11 19788600 19809400 Low Mappability
11 20310000 20312000 High Signal Region
11 20377900 20380400 High Signal Region
11 22322000 22340700 Low Mappability
11 22395200 22432900 Low Mappability
11 22534700 22537000 Low Mappability
11 23218500 23258100 Low Mappability
11 23522600 23552900 High Signal Region
11 24527400 24529500 Low Mappability
11 25196800 25217300 High Signal Region
11 25796400 25802200 Low Mappability
11 26898500 26900500 High Signal Region
11 27525200 27541400 High Signal Region
11 28097200 28104500 Low Mappability
11 29064100 29129900 Low Mappability
11 29259900 29291300 High Signal Region
11 29586000 29592400 Low Mappability
11 30511100 30535400 High Signal Region
11 31343800 31345700 Low Mappability
11 33062300 33068800 Low Mappability
11 34541000 34683100 High Signal Region
11 37482400 37484900 High Signal Region
11 40230800 40248400 High Signal Region
11 40625500 40640300 Low Mappability
11 40796600 40860600 High Signal Region
11 40887700 40915600 High Signal Region
11 41631700 41633600 High Signal Region
11 43237300 43239300 Low Mappability
11 43286400 43329800 High Signal Region
11 43454800 43462300 Low Mappability
11 43659700 43682100 Low Mappability
11 45584200 45655700 Low Mappability
11 46412300 46415000 Low Mappability
11 46492800 46514400 Low Mappability
11 47847500 47860600 High Signal Region
11 48451800 48536100 High Signal Region
11 48929800 49060400 Low Mappability
11 50445100 50469600 High Signal Region
11 51437600 51456700 High Signal Region
11 51664900 51690400 Low Mappability
11 54135500 54141600 High Signal Region
11 54576500 54583300 Low Mappability
11 55240500 55248100 Low Mappability
11 56588500 56594500 High Signal Region
11 57301700 57303600 High Signal Region
11 60558900 60699000 Low Mappability
11 61407400 61427800 Low Mappability
11 61593700 61596500 Low Mappability
11 62879300 62901500 High Signal Region
11 63467600 63475000 Low Mappability
11 64568100 64574200 High Signal Region
11 64681700 64683600 Low Mappability
11 64791900 64827100 Low Mappability
11 65451700 65458800 Low Mappability
11 66629900 66634100 High Signal Region
11 66947700 66958600 Low Mappability
11 67866400 67872800 Low Mappability
11 70155800 70162400 Low Mappability
11 71505700 71512100 Low Mappability
11 71875200 71881700 Low Mappability
11 73436900 73439100 Low Mappability
11 74128800 74136200 Low Mappability
11 74199900 74226800 Low Mappability
11 74301700 74319600 High Signal Region
11 74540000 74548400 Low Mappability
11 74884300 74899000 Low Mappability
11 76828100 76868600 Low Mappability
11 77255000 77257100 Low Mappability
11 79845100 79847300 Low Mappability
11 79872400 79877100 Low Mappability
11 79917300 79920800 Low Mappability
11 81545400 81552800 Low Mappability
11 82123300 82144400 High Signal Region
11 82333900 82338400 Low Mappability
11 83050300 83093600 High Signal Region
11 83126000 83172300 Low Mappability
11 85046500 85067800 High Signal Region
11 85285400 85292700 High Signal Region
11 88910900 88917600 Low Mappability
11 88965900 88971900 High Signal Region
11 89080800 89101300 High Signal Region
11 90504000 90510500 High Signal Region
11 90829400 90835000 Low Mappability
11 90901700 90908400 Low Mappability
11 90958500 91026800 Low Mappability
11 91047200 91049300 Low Mappability
11 92099000 92108200 High Signal Region
11 93409300 93428900 High Signal Region
11 94622900 94629900 Low Mappability
11 96065000 96093900 High Signal Region
11 98586900 98673900 Low Mappability
11 99712600 99717300 High Signal Region
11 100662800 100669700 Low Mappability
11 101731800 101741400 High Signal Region
11 102992300 103049900 Low Mappability
11 104239000 104242600 Low Mappability
11 106028100 106037400 High Signal Region
11 106254800 106297600 High Signal Region
11 106943500 106950100 Low Mappability
11 107188200 107200400 High Signal Region
11 107281300 107283200 High Signal Region
11 108377600 108404500 Low Mappability
11 108649800 108655400 Low Mappability
11 109010700 109024400 High Signal Region
11 109998500 110024600 Low Mappability
11 110421300 110423200 High Signal Region
11 111182400 111189800 Low Mappability
11 111215500 111234900 Low Mappability
11 111353300 111360000 Low Mappability
11 111855400 111857100 High Signal Region
11 112010600 112016400 High Signal Region
11 114456300 114462800 Low Mappability
11 115014300 115046900 Low Mappability
11 115611200 115665700 High Signal Region
11 115754800 115766900 Low Mappability
11 116389300 116395200 Low Mappability
11 116742700 116792800 Low Mappability
11 117499800 117505100 Low Mappability
11 119299800 119340300 Low Mappability
11 120305300 120357300 Low Mappability
11 120515100 120644700 High Signal Region
11 121069800 121075100 High Signal Region
11 121203000 121207500 Low Mappability
11 121396100 121422700 Low Mappability
11 121611900 121614000 Low Mappability
11 121981400 122082500 High Signal Region
12 0 3070900 High Signal Region
12 3102800 3111000 High Signal Region
12 4110500 4112400 High Signal Region
12 4218500 4235300 High Signal Region
12 4751600 4790100 High Signal Region
12 5050300 5065400 High Signal Region
12 6514000 6525100 High Signal Region
12 6606500 6612600 High Signal Region
12 7447300 7449900 High Signal Region
12 7801900 7808600 High Signal Region
12 7925300 7939600 High Signal Region
12 8572000 8640600 High Signal Region
12 10693000 10704200 High Signal Region
12 10961300 11004600 High Signal Region
12 11187600 11194100 High Signal Region
12 11642900 11658000 High Signal Region
12 12092500 12097600 High Signal Region
12 14844600 14848200 High Signal Region
12 15026600 15032400 High Signal Region
12 15252700 15259600 High Signal Region
12 15866100 15871800 High Signal Region
12 16746900 16748800 High Signal Region
12 17116400 17129400 High Signal Region
12 17243500 17248500 High Signal Region
12 18340700 18354800 High Signal Region
12 18856500 18909700 High Signal Region
12 19312600 19413500 High Signal Region
12 19442600 19590100 High Signal Region
12 19627700 19633600 High Signal Region
12 19777500 19781600 High Signal Region
12 19879300 19901200 High Signal Region
12 19931800 19948600 High Signal Region
12 20031900 20205100 High Signal Region
12 20225600 20298300 High Signal Region
12 21914300 21916000 Low Mappability
12 21972100 21987900 High Signal Region
12 22021600 22680500 Low Mappability
12 22896100 22902300 High Signal Region
12 23140700 23225200 High Signal Region
12 23283500 24030600 High Signal Region
12 24295300 24365100 Low Mappability
12 24692300 24727100 High Signal Region
12 25591800 25595300 Low Mappability
12 25840400 25842100 High Signal Region
12 27556800 27592000 High Signal Region
12 28491400 28494000 High Signal Region
12 28954800 28964000 High Signal Region
12 29379500 29400800 High Signal Region
12 30965100 31016300 High Signal Region
12 32020400 32032500 Low Mappability
12 32217700 32219200 High Signal Region
12 33388100 33410100 Low Mappability
12 33748900 33771800 High Signal Region
12 33869500 33880600 High Signal Region
12 34056800 34074100 High Signal Region
12 34128700 34139700 High Signal Region
12 34623000 34629000 Low Mappability
12 35783900 35814400 High Signal Region
12 36099400 36107200 High Signal Region
12 36679100 36700200 Low Mappability
12 36952200 36957900 High Signal Region
12 38746900 38749300 High Signal Region
12 41363500 41385500 High Signal Region
12 41502600 41516100 High Signal Region
12 41860000 41870200 High Signal Region
12 42124500 42126300 High Signal Region
12 42437900 42443400 High Signal Region
12 42666800 42690800 High Signal Region
12 43335600 43349300 High Signal Region
12 43659100 43675300 High Signal Region
12 43953900 43986900 High Signal Region
12 44064500 44070600 High Signal Region
12 44765600 44795900 Low Mappability
12 45768700 45773700 High Signal Region
12 45949200 45962200 High Signal Region
12 46707000 46709200 High Signal Region
12 47027300 47039300 High Signal Region
12 47280500 47286800 High Signal Region
12 47328600 47331300 High Signal Region
12 47646800 47648300 High Signal Region
12 47833000 47834900 High Signal Region
12 47995600 47997600 High Signal Region
12 48842900 48849500 High Signal Region
12 49124800 49155700 High Signal Region
12 49245200 49272100 High Signal Region
12 49606200 49612000 High Signal Region
12 50784600 50789900 High Signal Region
12 51486000 51492000 High Signal Region
12 52157900 52176400 High Signal Region
12 52200400 52223200 High Signal Region
12 52579600 52581200 High Signal Region
12 52730000 52735400 Low Mappability
12 52906200 52952300 High Signal Region
12 54358500 54369200 High Signal Region
12 54705400 54743600 High Signal Region
12 55079600 55267300 Low Mappability
12 56104100 56110600 Low Mappability
12 56423700 56425000 High Signal Region
12 56747800 56752200 High Signal Region
12 56911000 56914000 High Signal Region
12 58294800 58339800 High Signal Region
12 58659000 58692900 High Signal Region
12 58858800 58867600 High Signal Region
12 59034800 59039300 Low Mappability
12 59112800 59124700 High Signal Region
12 59270000 59276700 High Signal Region
12 59297800 59323200 High Signal Region
12 59601000 59605800 High Signal Region
12 60069500 60084400 High Signal Region
12 60501200 60506200 High Signal Region
12 61044200 61045300 High Signal Region
12 61289100 61293700 High Signal Region
12 61892600 61896100 High Signal Region
12 61964500 61971300 High Signal Region
12 62035300 62090200 High Signal Region
12 62959800 62999500 High Signal Region
12 63041800 63048200 High Signal Region
12 63289500 63322400 High Signal Region
12 63728400 63745100 High Signal Region
12 63838200 63840100 High Signal Region
12 65260100 65292400 High Signal Region
12 65784500 65808300 High Signal Region
12 66103800 66127200 High Signal Region
12 67058200 67060800 High Signal Region
12 67433500 67459300 High Signal Region
12 67519200 67571500 High Signal Region
12 67828900 67836600 High Signal Region
12 68696500 68711800 High Signal Region
12 68745100 68750600 Low Mappability
12 69059900 69061300 High Signal Region
12 69653100 69657800 High Signal Region
12 70641800 70668400 Low Mappability
12 71077100 71093600 Low Mappability
12 71589600 71596000 High Signal Region
12 72203000 72209300 High Signal Region
12 72634700 72641300 High Signal Region
12 74620800 74642100 High Signal Region
12 74775800 74778200 High Signal Region
12 74803000 74805400 High Signal Region
12 74857200 74862700 High Signal Region
12 75241800 75248400 High Signal Region
12 77160700 77166000 High Signal Region
12 77383500 77411300 High Signal Region
12 77547200 77553900 High Signal Region
12 78260000 78373200 High Signal Region
12 78462400 78468500 High Signal Region
12 80417200 80449700 High Signal Region
12 80894500 80916600 High Signal Region
12 81550400 81555100 High Signal Region
12 81985400 82064000 Low Mappability
12 83093000 83094900 High Signal Region
12 85401000 85408600 High Signal Region
12 87585600 87771500 Low Mappability
12 87802800 88006400 High Signal Region
12 88119800 88169700 Low Mappability
12 88229600 88312400 High Signal Region
12 88493200 88516700 Low Mappability
12 91221400 91256000 High Signal Region
12 91439200 91475500 High Signal Region
12 92393800 92395800 Low Mappability
12 92839700 92892700 High Signal Region
12 93233800 93265600 High Signal Region
12 93564200 93590500 High Signal Region
12 93915400 93951600 High Signal Region
12 94268500 94273900 High Signal Region
12 94550200 94556100 High Signal Region
12 94694300 94713700 High Signal Region
12 95976100 96021400 High Signal Region
12 97038100 97062700 High Signal Region
12 97616600 97622400 High Signal Region
12 98173700 98176600 High Signal Region
12 99644200 99649400 High Signal Region
12 100490600 100492300 High Signal Region
12 100766900 100825300 High Signal Region
12 101427900 101453500 High Signal Region
12 101839700 101849500 High Signal Region
12 102892000 102893900 High Signal Region
12 103458100 103472900 High Signal Region
12 103776900 103813700 High Signal Region
12 105300300 105307000 High Signal Region
12 105435200 105437100 High Signal Region
12 105523800 105525700 High Signal Region
12 105628200 105631400 High Signal Region
12 108078800 108084400 High Signal Region
12 109901900 109909200 Low Mappability
12 110011800 110013700 High Signal Region
12 111388200 111417100 High Signal Region
12 112542200 112548700 High Signal Region
12 112775700 112830900 Low Mappability
12 113423500 113461500 High Signal Region
12 114584600 114597100 High Signal Region
12 114941500 114943900 High Signal Region
12 115725800 115748700 High Signal Region
12 116796500 116853000 High Signal Region
12 118341100 118358400 High Signal Region
12 118794900 118797400 High Signal Region
12 119013600 119018100 High Signal Region
12 119554500 119598100 High Signal Region
12 119659100 119670900 High Signal Region
12 120023800 120129000 High Signal Region
13 0 3038200 High Signal Region
13 3350900 3378900 High Signal Region
13 3404500 3438200 High Signal Region
13 3901100 3903100 Low Mappability
13 4762900 4770300 High Signal Region
13 5171400 5178400 High Signal Region
13 7601300 7604100 High Signal Region
13 7806100 7810900 High Signal Region
13 7893500 7899700 High Signal Region
13 9828900 9855900 High Signal Region
13 10174800 10181100 Low Mappability
13 12684400 13073000 High Signal Region
13 13752100 13774000 High Signal Region
13 13859900 13907900 High Signal Region
13 13981000 13983000 High Signal Region
13 14690600 14777500 Low Mappability
13 18932700 18963600 Low Mappability
13 21753300 21847200 Low Mappability
13 23620800 23647900 Low Mappability
13 25006900 25051500 High Signal Region
13 26440600 26448200 High Signal Region
13 27164600 27169100 High Signal Region
13 27875800 27888500 High Signal Region
13 29880700 29886800 Low Mappability
13 32889400 32895200 High Signal Region
13 33280200 33319400 High Signal Region
13 33350500 33491800 High Signal Region
13 35687400 35695700 High Signal Region
13 36794200 36797400 High Signal Region
13 37036700 37043900 High Signal Region
13 38633900 38659300 Low Mappability
13 42435800 42437700 High Signal Region
13 44868600 44870900 High Signal Region
13 46316600 46324000 High Signal Region
13 50633400 50741800 High Signal Region
13 53269000 53270900 High Signal Region
13 60675600 60682600 High Signal Region
13 62291600 62346800 Low Mappability
13 62409800 62426300 High Signal Region
13 63142500 63184600 High Signal Region
13 64878100 64885300 High Signal Region
13 65352900 66254300 Low Mappability
13 71381400 71387500 High Signal Region
13 74521500 74565200 High Signal Region
13 74684000 74712200 High Signal Region
13 76472300 76501300 High Signal Region
13 77304000 77305900 High Signal Region
13 77430600 77440000 High Signal Region
13 79563400 79570800 High Signal Region
13 80276300 80279400 High Signal Region
13 80489100 80491400 High Signal Region
13 83419000 83444300 High Signal Region
13 85125800 85145900 High Signal Region
13 86149500 86190600 High Signal Region
13 86502700 86511700 High Signal Region
13 88324900 88345400 High Signal Region
13 92599100 92625400 Low Mappability
13 93279200 93294800 High Signal Region
13 93650100 93651500 High Signal Region
13 93940300 93955300 High Signal Region
13 94016300 94020800 High Signal Region
13 97189600 97206100 High Signal Region
13 98418200 98420500 Low Mappability
13 99774000 99792100 High Signal Region
13 102381900 102387900 High Signal Region
13 105123500 105128600 Low Mappability
13 107839000 107860300 Low Mappability
13 110602100 110615800 High Signal Region
13 110729600 110745400 High Signal Region
13 111187700 111189500 High Signal Region
13 111499700 111515900 Low Mappability
13 112577200 112595200 High Signal Region
13 113171200 113173100 High Signal Region
13 113272600 113310700 High Signal Region
13 115498200 115504200 High Signal Region
13 115741300 115743200 Low Mappability
13 116191900 116193900 High Signal Region
13 119188100 119230700 High Signal Region
13 119486800 119618500 High Signal Region
13 119660800 119674100 High Signal Region
13 119899200 120147600 Low Mappability
13 120320500 120421600 High Signal Region
14 0 4323000 High Signal Region
14 4372100 4741400 High Signal Region
14 4762800 5839200 High Signal Region
14 5959700 6479300 High Signal Region
14 6500100 6791800 High Signal Region
14 6993800 7734200 High Signal Region
14 7869900 7872200 High Signal Region
14 8005200 8018900 High Signal Region
14 8285700 8287800 High Signal Region
14 8652200 8658800 Low Mappability
14 10086500 10118400 High Signal Region
14 10178800 10198700 Low Mappability
14 11046200 11050200 High Signal Region
14 12536700 12538700 High Signal Region
14 14333600 14340200 High Signal Region
14 15460700 15467200 High Signal Region
14 16907800 16914000 High Signal Region
14 16937900 16941100 High Signal Region
14 18487900 18494100 High Signal Region
14 19251900 19255700 High Signal Region
14 19277200 19279100 High Signal Region
14 19414800 19633500 High Signal Region
14 21360400 21366100 High Signal Region
14 21878600 21884500 High Signal Region
14 22542900 22570000 High Signal Region
14 22902100 22934800 High Signal Region
14 25875200 26292200 High Signal Region
14 26946900 26948800 High Signal Region
14 29001300 29003200 Low Mappability
14 29343900 29345700 Low Mappability
14 30748800 30754700 High Signal Region
14 31919300 31923900 High Signal Region
14 32115300 32120500 Low Mappability
14 33667700 33670000 Low Mappability
14 33981000 33987500 Low Mappability
14 35275300 35281500 High Signal Region
14 35709400 35722200 High Signal Region
14 36429100 36440100 High Signal Region
14 37229100 37260800 Low Mappability
14 37619400 37635200 Low Mappability
14 38086800 38116800 High Signal Region
14 38280800 38283100 High Signal Region
14 38455100 38462200 Low Mappability
14 39580800 39607200 High Signal Region
14 39731900 39737200 High Signal Region
14 39905500 39911100 High Signal Region
14 41053200 41061900 Low Mappability
14 41326900 43109000 High Signal Region
14 43132400 43668900 High Signal Region
14 43803900 43850200 High Signal Region
14 44149300 44152100 High Signal Region
14 44273800 44343500 High Signal Region
14 44514200 44516000 Low Mappability
14 45726200 45753500 High Signal Region
14 45811900 45813800 High Signal Region
14 46269900 46274300 High Signal Region
14 47609500 47630400 High Signal Region
14 50538900 50606000 High Signal Region
14 50626200 50638500 High Signal Region
14 51472000 51515400 High Signal Region
14 51730700 51768100 High Signal Region
14 51814200 51837200 High Signal Region
14 52821200 53035800 Low Mappability
14 53146700 53340000 High Signal Region
14 53475200 53479600 High Signal Region
14 53515600 53530500 Low Mappability
14 56447800 56455700 High Signal Region
14 56693100 56695000 High Signal Region
14 58052600 58059800 Low Mappability
14 58462700 58464600 Low Mappability
14 58657800 58659700 High Signal Region
14 58831400 58833300 High Signal Region
14 59250300 59270000 High Signal Region
14 59488900 59490800 High Signal Region
14 59980800 59995700 High Signal Region
14 60328300 60357300 High Signal Region
14 60960000 60961900 Low Mappability
14 61580500 61586700 High Signal Region
14 61855000 61856300 High Signal Region
14 62107300 62126200 High Signal Region
14 64290100 64292500 High Signal Region
14 64463300 64478500 Low Mappability
14 65128900 65135300 Low Mappability
14 66427000 66428400 High Signal Region
14 68232600 68278200 High Signal Region
14 69161000 69163400 High Signal Region
14 70974500 70975600 High Signal Region
14 71121300 71126700 High Signal Region
14 71449700 71453700 High Signal Region
14 71783600 71804000 High Signal Region
14 72900100 72921400 High Signal Region
14 73644600 73679900 High Signal Region
14 73847900 73861200 High Signal Region
14 74039300 74066900 High Signal Region
14 74124400 74138500 High Signal Region
14 74435600 74447800 High Signal Region
14 75425300 75440500 High Signal Region
14 78162300 78168200 High Signal Region
14 78401700 78403200 High Signal Region
14 79145300 79196400 High Signal Region
14 80148100 80150800 High Signal Region
14 80422800 80439400 High Signal Region
14 80622600 80627700 High Signal Region
14 81333200 81337500 High Signal Region
14 81495300 81519300 High Signal Region
14 82077600 82084900 High Signal Region
14 82846900 82867200 High Signal Region
14 82958700 82964100 High Signal Region
14 83292900 83306500 High Signal Region
14 83507000 83512600 High Signal Region
14 84354700 84409800 High Signal Region
14 84855100 84881600 Low Mappability
14 85177800 85203300 Low Mappability
14 85521200 85535200 Low Mappability
14 86198000 86200000 High Signal Region
14 86590500 86614400 High Signal Region
14 87354600 87373000 High Signal Region
14 87671400 87677500 High Signal Region
14 87790500 87852200 High Signal Region
14 88450200 88453600 High Signal Region
14 88478400 88480300 High Signal Region
14 90018300 90019500 High Signal Region
14 90294700 90301800 High Signal Region
14 90910200 90912200 High Signal Region
14 91415900 91418400 High Signal Region
14 91510800 91514900 High Signal Region
14 91672700 91694800 High Signal Region
14 91951700 91976400 High Signal Region
14 92032500 92040900 High Signal Region
14 92383600 92389900 High Signal Region
14 92411600 92432900 High Signal Region
14 92792600 92798500 High Signal Region
14 92921100 92953200 High Signal Region
14 93017600 93020400 High Signal Region
14 93355600 93360200 High Signal Region
14 94319700 94327000 High Signal Region
14 95561600 95567600 High Signal Region
14 96048000 96054300 High Signal Region
14 96093600 96116100 High Signal Region
14 97323800 97326500 High Signal Region
14 98226800 98237000 High Signal Region
14 98731900 98757200 High Signal Region
14 99207100 99208200 High Signal Region
14 99649700 99655500 High Signal Region
14 101076400 101098900 Low Mappability
14 101404800 101414800 High Signal Region
14 102548900 102565300 High Signal Region
14 102755800 102762600 High Signal Region
14 103300300 103302400 High Signal Region
14 103858600 103872900 High Signal Region
14 103999500 104025500 High Signal Region
14 104104800 104128100 Low Mappability
14 104704500 104716800 High Signal Region
14 105758200 105764900 Low Mappability
14 105911400 105978300 High Signal Region
14 106002700 106005700 Low Mappability
14 106301000 106352700 High Signal Region
14 106444800 106483100 Low Mappability
14 106722600 106728700 High Signal Region
14 106895300 106897000 Low Mappability
14 108115100 108174900 Low Mappability
14 108283900 108303500 High Signal Region
14 109675300 109681200 High Signal Region
14 109911500 109917800 High Signal Region
14 110057000 110108200 Low Mappability
14 110356200 110373800 High Signal Region
14 110492000 110495700 Low Mappability
14 110906100 110908200 High Signal Region
14 110992800 110994500 High Signal Region
14 111903200 111909800 High Signal Region
14 112074600 112092300 High Signal Region
14 112210500 112215800 High Signal Region
14 112285400 112291900 High Signal Region
14 112332800 112340000 Low Mappability
14 112517900 112519900 High Signal Region
14 112627800 112663100 Low Mappability
14 114505900 114512900 High Signal Region
14 114822000 114823900 Low Mappability
14 115109700 115117400 High Signal Region
14 115272500 115280200 High Signal Region
14 115379200 115385600 High Signal Region
14 115911100 115912900 High Signal Region
14 115958100 115965000 High Signal Region
14 116402700 116407700 High Signal Region
14 116817000 116822900 High Signal Region
14 117285800 117292800 High Signal Region
14 118144700 118168500 Low Mappability
14 119286000 119287900 High Signal Region
14 120180000 120202600 High Signal Region
14 120742600 120749700 High Signal Region
14 120777500 120802300 High Signal Region
14 121007000 121010900 Low Mappability
14 122502500 122534800 High Signal Region
14 123349400 123351300 Low Mappability
14 123412000 123452600 High Signal Region
14 123674600 123695600 High Signal Region
14 124334000 124340200 High Signal Region
14 124415600 124436400 High Signal Region
14 124491600 124497700 High Signal Region
14 124739500 124902200 High Signal Region
15 0 3125600 High Signal Region
15 3150900 3170400 High Signal Region
15 3313900 3336200 High Signal Region
15 3360500 3363700 High Signal Region
15 3538600 3551000 High Signal Region
15 3712200 3732700 High Signal Region
15 3793500 3823000 High Signal Region
15 4155900 4160900 High Signal Region
15 4278500 4284100 High Signal Region
15 4852000 4894600 Low Mappability
15 4980200 4987600 Low Mappability
15 5369000 5385500 High Signal Region
15 5681700 5690400 High Signal Region
15 5910000 5911700 High Signal Region
15 5993500 5995400 High Signal Region
15 6074100 6087100 Low Mappability
15 6192800 6200000 Low Mappability
15 6316000 6317900 High Signal Region
15 6510500 6539100 High Signal Region
15 6674800 6701400 High Signal Region
15 6801200 6808300 High Signal Region
15 7539900 7548600 Low Mappability
15 7800800 7803000 Low Mappability
15 7849400 7855600 High Signal Region
15 7904400 7929500 Low Mappability
15 8517500 8520400 High Signal Region
15 8548000 8576100 Low Mappability
15 8800200 8808700 High Signal Region
15 8985200 9054800 High Signal Region
15 9219000 9224900 Low Mappability
15 9293200 9333300 High Signal Region
15 9379300 9409100 High Signal Region
15 9437100 9443600 High Signal Region
15 9536500 9554100 High Signal Region
15 9992700 10045700 High Signal Region
15 10579600 10591500 Low Mappability
15 10753400 10810200 High Signal Region
15 10835200 10854700 Low Mappability
15 11921000 11933300 High Signal Region
15 12055800 12063200 Low Mappability
15 12526800 12531900 Low Mappability
15 12872000 12873900 High Signal Region
15 12932300 12934200 Low Mappability
15 13919500 13948300 High Signal Region
15 14414600 14439100 Low Mappability
15 14722200 14732900 High Signal Region
15 14873900 14902400 High Signal Region
15 15043600 15059700 High Signal Region
15 15525500 15551900 High Signal Region
15 16168200 16186400 High Signal Region
15 16303700 16309500 High Signal Region
15 16716400 16717500 High Signal Region
15 16901300 16907100 High Signal Region
15 16939800 16955100 Low Mappability
15 17139000 17169100 High Signal Region
15 17562100 17581400 High Signal Region
15 18314600 18325000 High Signal Region
15 19038400 19063800 Low Mappability
15 19402600 19405500 High Signal Region
15 19448100 19453900 High Signal Region
15 19557200 19578000 High Signal Region
15 19626800 19631800 High Signal Region
15 19678400 19685800 High Signal Region
15 20063000 20067500 High Signal Region
15 20155100 20170700 Low Mappability
15 20474900 20510100 High Signal Region
15 20531400 20537100 High Signal Region
15 20821500 20826700 High Signal Region
15 20972700 20978300 Low Mappability
15 21114000 21115900 High Signal Region
15 21262100 21268500 Low Mappability
15 21423200 21487200 High Signal Region
15 21655500 21657500 High Signal Region
15 21815500 21820800 High Signal Region
15 21853700 21892400 High Signal Region
15 22268700 22293500 High Signal Region
15 22751400 22756700 Low Mappability
15 22799300 22809700 Low Mappability
15 23240200 23255600 Low Mappability
15 23465300 23467800 High Signal Region
15 23886000 23887900 Low Mappability
15 23926900 23939700 High Signal Region
15 24309300 24325700 Low Mappability
15 24761100 24766700 High Signal Region
15 24801600 24837300 High Signal Region
15 24880900 24898600 Low Mappability
15 25051400 25065200 Low Mappability
15 26112700 26118900 High Signal Region
15 26905000 26919300 Low Mappability
15 27286100 27326800 High Signal Region
15 27384100 27390300 Low Mappability
15 27638200 27640500 High Signal Region
15 28564400 28578800 High Signal Region
15 29285200 29291500 Low Mappability
15 29347600 29395600 High Signal Region
15 29463900 29470200 High Signal Region
15 29969800 30001400 High Signal Region
15 30117700 30126200 High Signal Region
15 30441400 30448200 Low Mappability
15 30747900 30755000 High Signal Region
15 30996700 31016300 High Signal Region
15 31066700 31083700 High Signal Region
15 32783900 32806700 High Signal Region
15 32832800 32880300 High Signal Region
15 33138700 33140800 Low Mappability
15 33308700 33310800 Low Mappability
15 33444200 33454100 High Signal Region
15 33710200 33745700 High Signal Region
15 33781400 33849400 High Signal Region
15 33869800 33884700 High Signal Region
15 34494500 34502100 Low Mappability
15 34763100 34769400 High Signal Region
15 34987600 34992800 High Signal Region
15 35013200 35015400 High Signal Region
15 35366800 35406000 High Signal Region
15 36715200 36737400 High Signal Region
15 36966700 36997400 Low Mappability
15 37072900 37150800 Low Mappability
15 38462300 38484300 Low Mappability
15 39172900 39178300 Low Mappability
15 39335600 39348800 Low Mappability
15 39496100 39499100 High Signal Region
15 39695600 39718600 Low Mappability
15 40049600 40056000 High Signal Region
15 40086800 40101400 High Signal Region
15 41531400 41533200 High Signal Region
15 41890400 41896900 Low Mappability
15 42354900 42361100 High Signal Region
15 42925300 42942800 High Signal Region
15 43287300 43346300 High Signal Region
15 44469100 44476400 High Signal Region
15 44649000 44659600 Low Mappability
15 44723200 44728200 Low Mappability
15 44769700 44796100 High Signal Region
15 45005100 45009300 High Signal Region
15 45194600 45197100 High Signal Region
15 45577500 45590900 High Signal Region
15 45635600 45650500 High Signal Region
15 45774400 45779700 High Signal Region
15 45890700 45932500 High Signal Region
15 46255700 46257800 Low Mappability
15 46355600 46368400 High Signal Region
15 46502200 46506800 Low Mappability
15 46562500 46566200 Low Mappability
15 47232800 47256000 High Signal Region
15 47356500 47363700 Low Mappability
15 47539000 47555300 High Signal Region
15 48666900 48671000 High Signal Region
15 49283300 49299700 High Signal Region
15 49322600 49327300 Low Mappability
15 50426100 50442800 High Signal Region
15 50557700 50642600 High Signal Region
15 51113200 51117800 High Signal Region
15 51531900 51533900 Low Mappability
15 52125800 52131200 High Signal Region
15 52329800 52353100 High Signal Region
15 53039200 53044200 Low Mappability
15 53831000 53834900 High Signal Region
15 53870700 53872700 High Signal Region
15 53918300 53929500 High Signal Region
15 54180700 54211500 Low Mappability
15 56032900 56038200 High Signal Region
15 56175800 56183100 Low Mappability
15 56363800 56367900 High Signal Region
15 56400500 56402200 High Signal Region
15 56941600 56993500 High Signal Region
15 57279500 57285000 High Signal Region
15 57412200 57433600 High Signal Region
15 57889500 57913700 Low Mappability
15 58437200 58441100 High Signal Region
15 59421400 59435400 Low Mappability
15 59850100 59875200 Low Mappability
15 60153100 60203900 High Signal Region
15 60592000 60594300 Low Mappability
15 60931800 60986500 High Signal Region
15 61148600 61150700 High Signal Region
15 61903100 61915500 High Signal Region
15 62367600 62370100 High Signal Region
15 62553200 62555200 High Signal Region
15 62686500 62693700 High Signal Region
15 63329400 63346600 Low Mappability
15 63626000 63627900 High Signal Region
15 63791700 63796000 High Signal Region
15 63837600 63922800 High Signal Region
15 64591700 64598200 Low Mappability
15 64673500 64681900 High Signal Region
15 65115600 65123500 Low Mappability
15 65598500 65604500 High Signal Region
15 65666600 65673800 High Signal Region
15 65714400 65753500 High Signal Region
15 66045100 66065700 High Signal Region
15 66208300 66210200 High Signal Region
15 68136300 68137800 Low Mappability
15 68980000 68986500 High Signal Region
15 69122300 69164500 High Signal Region
15 69264900 69268800 High Signal Region
15 69390300 69409400 High Signal Region
15 69642000 69646000 High Signal Region
15 70083000 70088800 High Signal Region
15 70609300 70611100 High Signal Region
15 70896600 70914000 High Signal Region
15 71104600 71112200 High Signal Region
15 71206600 71237500 Low Mappability
15 73060200 73087900 Low Mappability
15 73373200 73378200 Low Mappability
15 73873000 73880400 Low Mappability
15 74360700 74368000 Low Mappability
15 74814300 74826700 Low Mappability
15 74992000 75104600 High Signal Region
15 75205600 75212800 Low Mappability
15 75298000 75299500 High Signal Region
15 75437000 75440500 High Signal Region
15 75523600 75529700 High Signal Region
15 76102000 76106500 High Signal Region
15 76559900 76577900 Low Mappability
15 76964600 76971400 Low Mappability
15 77336200 77439100 High Signal Region
15 77718300 77735600 Low Mappability
15 77895000 77934800 Low Mappability
15 79685000 79775700 Low Mappability
15 79869700 79892600 Low Mappability
15 79974400 79978400 Low Mappability
15 80232400 80267100 High Signal Region
15 81145400 81152000 Low Mappability
15 81492300 81523600 High Signal Region
15 82338000 82368000 Low Mappability
15 82590700 82608900 Low Mappability
15 82675500 82677200 High Signal Region
15 83172100 83202200 Low Mappability
15 84746600 84753000 Low Mappability
15 85176800 85196600 Low Mappability
15 85541200 85543100 High Signal Region
15 86193800 86196100 High Signal Region
15 86312100 86326400 Low Mappability
15 87293900 87301200 Low Mappability
15 87967000 87969000 High Signal Region
15 88779400 88783900 Low Mappability
15 88974800 88976800 High Signal Region
15 89597900 89621300 High Signal Region
15 89808500 89809700 High Signal Region
15 89943000 89982000 Low Mappability
15 90636400 90643600 Low Mappability
15 91115900 91134800 Low Mappability
15 91419400 91422200 High Signal Region
15 91720600 91723200 Low Mappability
15 91905900 91911200 High Signal Region
15 92470100 92475100 Low Mappability
15 92613700 92618300 Low Mappability
15 92722600 92730100 Low Mappability
15 92796100 92820000 Low Mappability
15 93044100 93062000 High Signal Region
15 93467800 93469500 Low Mappability
15 93867100 93873600 High Signal Region
15 94088400 94124100 High Signal Region
15 94150500 94156800 High Signal Region
15 94373000 94379600 High Signal Region
15 95087600 95092100 High Signal Region
15 95306000 95312300 High Signal Region
15 95729500 95756400 High Signal Region
15 96551700 96559500 Low Mappability
15 96977900 96983600 Low Mappability
15 97082100 97084300 High Signal Region
15 97472900 97487400 Low Mappability
15 99168800 99171900 High Signal Region
15 99552100 99553900 Low Mappability
15 100331500 100339800 Low Mappability
15 100360000 100379700 Low Mappability
15 100541700 100617400 Low Mappability
15 101655700 101662100 High Signal Region
15 102596800 102603200 High Signal Region
15 103271900 103277100 High Signal Region
15 103406700 103418500 High Signal Region
15 103606700 103611400 High Signal Region
15 103814500 104043600 High Signal Region
16 0 3427800 High Signal Region
16 3450300 3519700 Low Mappability
16 4300400 4366800 Low Mappability
16 4585000 4591300 High Signal Region
16 5708200 5710200 High Signal Region
16 7460800 7463600 High Signal Region
16 7937100 7958400 Low Mappability
16 8256700 8286200 High Signal Region
16 9577100 9579600 Low Mappability
16 10631200 10633200 Low Mappability
16 10974100 11013900 High Signal Region
16 11134600 11145200 High Signal Region
16 11248000 11249900 Low Mappability
16 11679900 11687500 Low Mappability
16 12327300 12345900 Low Mappability
16 12417900 12423400 High Signal Region
16 12829200 12831000 High Signal Region
16 12976200 12981700 Low Mappability
16 13087700 13107000 Low Mappability
16 13903200 13925900 Low Mappability
16 14316200 14341200 Low Mappability
16 15502700 15510100 Low Mappability
16 15741400 15757700 Low Mappability
16 17199900 17236000 High Signal Region
16 17751400 17761300 High Signal Region
16 17910400 17955500 High Signal Region
16 18532200 18534200 High Signal Region
16 18957500 18979200 High Signal Region
16 19334200 19375100 High Signal Region
16 19581200 19602400 Low Mappability
16 19711900 19748700 High Signal Region
16 19928600 19946300 Low Mappability
16 22923300 22929100 High Signal Region
16 26419300 26421200 High Signal Region
16 26808500 26814800 High Signal Region
16 27071900 27087600 High Signal Region
16 27212200 27218300 High Signal Region
16 28170600 28197500 High Signal Region
16 30828600 30830500 High Signal Region
16 31223800 31234300 Low Mappability
16 31339100 31358900 High Signal Region
16 31818700 31825200 Low Mappability
16 32147700 32153500 Low Mappability
16 32489700 32520100 Low Mappability
16 32579100 32598800 Low Mappability
16 33847200 33852600 Low Mappability
16 34581100 34591200 Low Mappability
16 34742000 34744000 High Signal Region
16 35980600 35983300 High Signal Region
16 36764900 36770500 Low Mappability
16 38714200 38721600 Low Mappability
16 39563700 39568200 High Signal Region
16 41270700 41273100 High Signal Region
16 42657300 42661200 High Signal Region
16 42773100 42779900 High Signal Region
16 42931600 42950000 High Signal Region
16 43764000 43771600 Low Mappability
16 44040400 44063900 Low Mappability
16 44709800 44726400 Low Mappability
16 44920200 44950700 Low Mappability
16 45292600 45293900 High Signal Region
16 45352100 45354000 High Signal Region
16 46364600 46369100 High Signal Region
16 47099100 47147300 High Signal Region
16 47552300 47564100 Low Mappability
16 48579900 48581300 Low Mappability
16 49024900 49031400 Low Mappability
16 49148400 49150300 Low Mappability
16 49447700 49489300 High Signal Region
16 50084900 50101400 Low Mappability
16 50909100 50926800 Low Mappability
16 51087100 51094300 Low Mappability
16 51945800 51980200 High Signal Region
16 53412000 53428900 High Signal Region
16 53571500 53595400 Low Mappability
16 54298300 54307600 Low Mappability
16 54861600 54869000 High Signal Region
16 54959000 54965200 High Signal Region
16 55647800 55681600 Low Mappability
16 56038100 56065100 Low Mappability
16 56988400 57008400 High Signal Region
16 57085500 57095800 High Signal Region
16 57390200 57392600 High Signal Region
16 57792800 57811700 Low Mappability
16 58310800 58343000 High Signal Region
16 58632300 58670400 Low Mappability
16 59121800 59129100 Low Mappability
16 59310100 59378100 High Signal Region
16 60921200 60970900 High Signal Region
16 61312500 61325200 Low Mappability
16 62564300 62599200 High Signal Region
16 62875900 62880400 Low Mappability
16 63114300 63151200 High Signal Region
16 63301300 63313600 High Signal Region
16 64384600 64425600 High Signal Region
16 65176900 65181400 Low Mappability
16 66229300 66247600 Low Mappability
16 67328200 67334700 High Signal Region
16 68272300 68274300 High Signal Region
16 70542300 70558300 Low Mappability
16 70633900 70639700 Low Mappability
16 70892400 70898400 High Signal Region
16 70976900 70982900 High Signal Region
16 71687000 71691500 Low Mappability
16 72019300 72023900 Low Mappability
16 72056200 72062100 High Signal Region
16 72724800 72730900 Low Mappability
16 73656700 73688600 High Signal Region
16 74771800 74781500 Low Mappability
16 76057000 76065000 Low Mappability
16 76487100 76519600 High Signal Region
16 76988700 76991600 High Signal Region
16 77116900 77121900 Low Mappability
16 78977100 79013600 High Signal Region
16 79368600 79376000 Low Mappability
16 79782000 79786700 High Signal Region
16 79943000 79948600 Low Mappability
16 80269400 80309700 Low Mappability
16 81071700 81079200 Low Mappability
16 81779900 81782000 High Signal Region
16 81859300 81865600 High Signal Region
16 82079700 82099600 High Signal Region
16 82237800 82243200 Low Mappability
16 82828200 82845600 High Signal Region
16 83077300 83081800 High Signal Region
16 83360600 83368000 Low Mappability
16 84260500 84283300 High Signal Region
16 84380600 84407600 High Signal Region
16 84440100 84446000 High Signal Region
16 85671600 85673000 High Signal Region
16 85713500 85720100 High Signal Region
16 86333000 86354300 High Signal Region
16 86539500 86570300 High Signal Region
16 86819800 86822100 High Signal Region
16 87055400 87060300 High Signal Region
16 87287400 87302500 Low Mappability
16 87372300 87391700 Low Mappability
16 88022900 88029900 High Signal Region
16 88790600 88797900 Low Mappability
16 88957900 88967800 High Signal Region
16 89145200 89196100 Low Mappability
16 89431800 89448400 Low Mappability
16 89636000 89642900 High Signal Region
16 89877500 89879700 High Signal Region
16 90056200 90072300 Low Mappability
16 90341200 90350100 Low Mappability
16 91533700 91551800 High Signal Region
16 92254500 92259400 Low Mappability
16 93581500 93622800 High Signal Region
16 93685800 93711200 High Signal Region
16 93785700 93790200 High Signal Region
16 93991400 93997900 High Signal Region
16 94258100 94282000 Low Mappability
16 95782000 95788900 High Signal Region
16 95991000 96010400 Low Mappability
16 97996400 98207700 High Signal Region
17 0 3039300 High Signal Region
17 3075400 3085400 High Signal Region
17 3378900 3380800 High Signal Region
17 5863900 5885100 High Signal Region
17 6219100 6717500 High Signal Region
17 6877300 7037900 High Signal Region
17 7302300 7430200 High Signal Region
17 7615300 7617200 High Signal Region
17 7950200 8052300 High Signal Region
17 11097900 11105100 High Signal Region
17 13018500 13469100 High Signal Region
17 13492200 13555800 High Signal Region
17 13584800 13656200 High Signal Region
17 14961200 15054300 Low Mappability
17 20859400 20865200 High Signal Region
17 23426600 23537000 High Signal Region
17 23730600 23732500 High Signal Region
17 24095300 24097300 High Signal Region
17 29101000 29109600 High Signal Region
17 31569500 31571400 High Signal Region
17 35367400 35480300 Low Mappability
17 36230300 36232500 High Signal Region
17 38498200 38500800 High Signal Region
17 39842000 39849700 High Signal Region
17 40422500 40427000 High Signal Region
17 50569500 50571400 High Signal Region
17 53034300 53056100 High Signal Region
17 53151500 53153500 High Signal Region
17 53807400 53820300 High Signal Region
17 54112300 54134200 High Signal Region
17 57368400 57399900 High Signal Region
17 62736600 62738500 High Signal Region
17 66798500 66800400 High Signal Region
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17 84458800 84464500 Low Mappability
17 85264100 85266000 High Signal Region
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18 3619800 3652100 Low Mappability
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18 3815100 3819300 High Signal Region
18 3873200 3889000 High Signal Region
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18 4658000 4664400 Low Mappability
18 4695200 4701800 Low Mappability
18 5499400 5502000 Low Mappability
18 5895900 5900400 Low Mappability
18 6043700 6046600 Low Mappability
18 6343100 6376400 Low Mappability
18 6663800 6669200 High Signal Region
18 6796200 6803600 Low Mappability
18 6853600 6868500 Low Mappability
18 7032800 7035500 High Signal Region
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18 8164900 8183000 High Signal Region
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18 8721900 8747000 High Signal Region
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18 9420000 9426100 High Signal Region
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18 13296400 13300000 High Signal Region
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18 15225500 15232800 High Signal Region
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gitextract_tbgkhg71/
├── .devcontainer/
│ └── devcontainer.json
├── .editorconfig
├── .gitattributes
├── .github/
│ ├── .dockstore.yml
│ ├── CONTRIBUTING.md
│ ├── ISSUE_TEMPLATE/
│ │ ├── bug_report.yml
│ │ ├── config.yml
│ │ └── feature_request.yml
│ ├── PULL_REQUEST_TEMPLATE.md
│ └── workflows/
│ ├── awsfulltest.yml
│ ├── awstest.yml
│ ├── branch.yml
│ ├── ci.yml
│ ├── clean-up.yml
│ ├── fix-linting.yml
│ ├── linting.yml
│ └── linting_comment.yml
├── .gitignore
├── .gitpod.yml
├── .nf-core.yml
├── .pre-commit-config.yaml
├── .prettierignore
├── .prettierrc.yml
├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets/
│ ├── adaptivecard.json
│ ├── bamtools_filter_pe.json
│ ├── bamtools_filter_se.json
│ ├── blacklists/
│ │ ├── old/
│ │ │ ├── GRCm38-blacklist.bed
│ │ │ ├── hg38-blacklist.bed
│ │ │ └── mm10-blacklist.bed
│ │ ├── v1.0/
│ │ │ ├── GRCh37-blacklist.v1.bed
│ │ │ └── hg19-blacklist.v1.bed
│ │ ├── v2.0/
│ │ │ ├── GRCm38-blacklist.v2.bed
│ │ │ ├── ce10-blacklist.v2.bed
│ │ │ ├── ce11-blacklist.v2.bed
│ │ │ ├── dm3-blacklist.v2.bed
│ │ │ ├── dm6-blacklist.v2.bed
│ │ │ ├── hg19-blacklist.v2.bed
│ │ │ ├── hg38-blacklist.v2.bed
│ │ │ └── mm10-blacklist.v2.bed
│ │ └── v3.0/
│ │ ├── GRCh38-blacklist.v3.bed
│ │ └── hg38-blacklist.v3.bed
│ ├── email_template.html
│ ├── email_template.txt
│ ├── methods_description_template.yml
│ ├── multiqc/
│ │ ├── merged_library_deseq2_clustering_header.txt
│ │ ├── merged_library_deseq2_pca_header.txt
│ │ ├── merged_library_frip_score_header.txt
│ │ ├── merged_library_peak_annotation_header.txt
│ │ ├── merged_library_peak_count_header.txt
│ │ ├── merged_replicate_deseq2_clustering_header.txt
│ │ ├── merged_replicate_deseq2_pca_header.txt
│ │ ├── merged_replicate_frip_score_header.txt
│ │ ├── merged_replicate_peak_annotation_header.txt
│ │ └── merged_replicate_peak_count_header.txt
│ ├── multiqc_config.yml
│ ├── samplesheet.csv
│ ├── schema_input.json
│ ├── sendmail_template.txt
│ └── slackreport.json
├── bin/
│ ├── bampe_rm_orphan.py
│ ├── check_samplesheet.py
│ ├── deseq2_qc.r
│ ├── get_autosomes.py
│ ├── gtf2bed
│ ├── igv_files_to_session.py
│ ├── macs2_merged_expand.py
│ ├── plot_homer_annotatepeaks.r
│ ├── plot_macs2_qc.r
│ └── plot_peak_intersect.r
├── conf/
│ ├── base.config
│ ├── igenomes.config
│ ├── modules.config
│ ├── test.config
│ ├── test_controls.config
│ └── test_full.config
├── docs/
│ ├── README.md
│ ├── output.md
│ └── usage.md
├── lib/
│ ├── NfcoreTemplate.groovy
│ ├── Utils.groovy
│ ├── WorkflowAtacseq.groovy
│ ├── WorkflowMain.groovy
│ └── nfcore_external_java_deps.jar
├── main.nf
├── modules/
│ ├── local/
│ │ ├── bam_remove_orphans.nf
│ │ ├── bamtools_filter.nf
│ │ ├── bedtools_genomecov.nf
│ │ ├── deseq2_qc.nf
│ │ ├── frip_score.nf
│ │ ├── genome_blacklist_regions.nf
│ │ ├── get_autosomes.nf
│ │ ├── gtf2bed.nf
│ │ ├── igv.nf
│ │ ├── macs2_consensus.nf
│ │ ├── multiqc.nf
│ │ ├── multiqc_custom_peaks.nf
│ │ ├── plot_homer_annotatepeaks.nf
│ │ ├── plot_macs2_qc.nf
│ │ ├── samplesheet_check.nf
│ │ ├── star_align.nf
│ │ ├── star_genomegenerate.nf
│ │ └── tss_extract.nf
│ └── nf-core/
│ ├── ataqv/
│ │ ├── ataqv/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── mkarv/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bowtie2/
│ │ ├── align/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── build/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bwa/
│ │ ├── index/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── mem/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── chromap/
│ │ ├── chromap/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── index/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── custom/
│ │ ├── dumpsoftwareversions/
│ │ │ ├── main.nf
│ │ │ ├── meta.yml
│ │ │ └── templates/
│ │ │ └── dumpsoftwareversions.py
│ │ └── getchromsizes/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── deeptools/
│ │ ├── computematrix/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── plotfingerprint/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── plotheatmap/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── plotprofile/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastqc/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── gffread/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── gunzip/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── homer/
│ │ └── annotatepeaks/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── khmer/
│ │ └── uniquekmers/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── macs2/
│ │ └── callpeak/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── picard/
│ │ ├── collectmultiplemetrics/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── markduplicates/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── mergesamfiles/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── preseq/
│ │ └── lcextrap/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── samtools/
│ │ ├── flagstat/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── idxstats/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── index/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ ├── sort/
│ │ │ ├── main.nf
│ │ │ └── meta.yml
│ │ └── stats/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── subread/
│ │ └── featurecounts/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── trimgalore/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── ucsc/
│ │ └── bedgraphtobigwig/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── umitools/
│ │ └── extract/
│ │ ├── main.nf
│ │ └── meta.yml
│ └── untar/
│ ├── main.nf
│ └── meta.yml
├── modules.json
├── nextflow.config
├── nextflow_schema.json
├── pyproject.toml
├── subworkflows/
│ ├── local/
│ │ ├── align_star.nf
│ │ ├── bam_bedgraph_bigwig_bedtools_ucsc.nf
│ │ ├── bam_filter_bamtools.nf
│ │ ├── bam_peaks_call_qc_annotate_macs2_homer.nf
│ │ ├── bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf
│ │ ├── bigwig_plot_deeptools.nf
│ │ ├── input_check.nf
│ │ └── prepare_genome.nf
│ └── nf-core/
│ ├── bam_markduplicates_picard/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bam_sort_stats_samtools/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── bam_stats_samtools/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastq_align_bowtie2/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastq_align_bwa/
│ │ ├── main.nf
│ │ └── meta.yml
│ ├── fastq_align_chromap/
│ │ ├── main.nf
│ │ └── meta.yml
│ └── fastq_fastqc_umitools_trimgalore/
│ ├── main.nf
│ └── meta.yml
├── tower.yml
└── workflows/
└── atacseq.nf
SYMBOL INDEX (15 symbols across 6 files) FILE: bin/bampe_rm_orphan.py function makedir (line 48) | def makedir(path): function bampe_rm_orphan (line 64) | def bampe_rm_orphan(BAMIn, BAMOut, onlyFRPairs=False): FILE: bin/check_samplesheet.py function parse_args (line 8) | def parse_args(args=None): function make_dir (line 19) | def make_dir(path): function print_error (line 28) | def print_error(error, context="Line", context_str=""): function check_samplesheet (line 38) | def check_samplesheet(file_in, file_out, with_control=False): function main (line 212) | def main(args=None): FILE: bin/get_autosomes.py function makedir (line 36) | def makedir(path): function get_autosomes (line 70) | def get_autosomes(FAIFile, OutFile): FILE: bin/igv_files_to_session.py function makedir (line 51) | def makedir(path): function igv_files_to_session (line 67) | def igv_files_to_session(XMLOut, ListFile, Genome, PathPrefix=""): FILE: bin/macs2_merged_expand.py function makedir (line 57) | def makedir(path): function macs2_merged_expand (line 79) | def macs2_merged_expand(MergedIntervalTxtFile, SampleNameList, OutFile, ... FILE: modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py function _make_versions_html (line 12) | def _make_versions_html(versions): function main (line 52) | def main():
Condensed preview — 204 files, each showing path, character count, and a content snippet. Download the .json file or copy for the full structured content (1,169K chars).
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},
{
"path": "conf/test_full.config",
"chars": 911,
"preview": "/*\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n Nextflow config file for"
},
{
"path": "docs/README.md",
"chars": 510,
"preview": "# nf-core/atacseq: Documentation\n\nThe nf-core/atacseq documentation is split into the following pages:\n\n- [Usage](usage."
},
{
"path": "docs/output.md",
"chars": 28863,
"preview": "# \n\n## Introduction\n\nThis document describes the output produced by t"
},
{
"path": "docs/usage.md",
"chars": 20350,
"preview": "# nf-core/atacseq: Usage\n\n## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/atacseq/"
},
{
"path": "lib/NfcoreTemplate.groovy",
"chars": 16618,
"preview": "//\n// This file holds several functions used within the nf-core pipeline template.\n//\n\nimport org.yaml.snakeyaml.Yaml\n\nc"
},
{
"path": "lib/Utils.groovy",
"chars": 2038,
"preview": "//\n// This file holds several Groovy functions that could be useful for any Nextflow pipeline\n//\n\nimport org.yaml.snakey"
},
{
"path": "lib/WorkflowAtacseq.groovy",
"chars": 7099,
"preview": "//\n// This file holds several functions specific to the workflow/atacseq.nf in the nf-core/atacseq pipeline\n//\n\nimport n"
},
{
"path": "lib/WorkflowMain.groovy",
"chars": 2516,
"preview": "//\n// This file holds several functions specific to the main.nf workflow in the nf-core/atacseq pipeline\n//\n\nimport next"
},
{
"path": "main.nf",
"chars": 3351,
"preview": "#!/usr/bin/env nextflow\n/*\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n "
},
{
"path": "modules/local/bam_remove_orphans.nf",
"chars": 1499,
"preview": "process BAM_REMOVE_ORPHANS {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::pysam=0.19.0 bioconda::"
},
{
"path": "modules/local/bamtools_filter.nf",
"chars": 1502,
"preview": "process BAMTOOLS_FILTER {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::bamtools=2.5.2 bioconda::s"
},
{
"path": "modules/local/bedtools_genomecov.nf",
"chars": 1305,
"preview": "process BEDTOOLS_GENOMECOV {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::bedtools=2.30.0\"\n co"
},
{
"path": "modules/local/deseq2_qc.nf",
"chars": 2691,
"preview": "process DESEQ2_QC {\n tag \"$meta.id\"\n label 'process_medium'\n\n // (Bio)conda packages have intentionally not bee"
},
{
"path": "modules/local/frip_score.nf",
"chars": 1390,
"preview": "process FRIP_SCORE {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::bedtools=2.30.0 bioconda::samto"
},
{
"path": "modules/local/genome_blacklist_regions.nf",
"chars": 1372,
"preview": "process GENOME_BLACKLIST_REGIONS {\n tag \"$sizes\"\n\n conda \"bioconda::bedtools=2.30.0\"\n container \"${ workflow.co"
},
{
"path": "modules/local/get_autosomes.nf",
"chars": 779,
"preview": "process GET_AUTOSOMES {\n tag \"$fai\"\n\n conda \"conda-forge::python=3.8.3\"\n container \"${ workflow.containerEngine"
},
{
"path": "modules/local/gtf2bed.nf",
"chars": 801,
"preview": "process GTF2BED {\n tag \"$gtf\"\n label 'process_low'\n\n conda \"conda-forge::perl=5.26.2\"\n container \"${ workflo"
},
{
"path": "modules/local/igv.nf",
"chars": 2433,
"preview": "process IGV {\n\n conda \"conda-forge::python=3.8.3\"\n container \"${ workflow.containerEngine == 'singularity' && !tas"
},
{
"path": "modules/local/macs2_consensus.nf",
"chars": 2562,
"preview": "process MACS2_CONSENSUS {\n tag \"$meta.id\"\n label 'process_long'\n\n conda \"conda-forge::biopython conda-forge::r-"
},
{
"path": "modules/local/multiqc.nf",
"chars": 2471,
"preview": "process MULTIQC {\n label 'process_medium'\n\n conda 'bioconda::multiqc=1.13'\n container \"${ workflow.containerEng"
},
{
"path": "modules/local/multiqc_custom_peaks.nf",
"chars": 1080,
"preview": "process MULTIQC_CUSTOM_PEAKS {\n tag \"$meta.id\"\n\n conda \"conda-forge::sed=4.7\"\n container \"${ workflow.container"
},
{
"path": "modules/local/plot_homer_annotatepeaks.nf",
"chars": 1636,
"preview": "process PLOT_HOMER_ANNOTATEPEAKS {\n label 'process_medium'\n\n conda \"conda-forge::r-base=4.0.3 conda-forge::r-resha"
},
{
"path": "modules/local/plot_macs2_qc.nf",
"chars": 1465,
"preview": "process PLOT_MACS2_QC {\n label 'process_medium'\n\n conda \"conda-forge::r-base=4.0.3 conda-forge::r-reshape2=1.4.4 c"
},
{
"path": "modules/local/samplesheet_check.nf",
"chars": 849,
"preview": "process SAMPLESHEET_CHECK {\n tag \"$samplesheet\"\n label 'process_single'\n\n conda \"conda-forge::python=3.8.3\"\n "
},
{
"path": "modules/local/star_align.nf",
"chars": 2481,
"preview": "process STAR_ALIGN {\n tag \"$meta.id\"\n label 'process_high'\n\n // Note: 2.7X indices incompatible with AWS iGenom"
},
{
"path": "modules/local/star_genomegenerate.nf",
"chars": 2150,
"preview": "process STAR_GENOMEGENERATE {\n tag \"$fasta\"\n label 'process_high'\n\n // Note: 2.7X indices incompatible with AWS"
},
{
"path": "modules/local/tss_extract.nf",
"chars": 776,
"preview": "process TSS_EXTRACT {\n\n conda \"conda-forge::sed=4.7\"\n container \"${ workflow.containerEngine == 'singularity' && !"
},
{
"path": "modules/nf-core/ataqv/ataqv/main.nf",
"chars": 1729,
"preview": "process ATAQV_ATAQV {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda 'bioconda::ataqv=1.3.1'\n container \"${"
},
{
"path": "modules/nf-core/ataqv/ataqv/meta.yml",
"chars": 2904,
"preview": "name: ataqv_ataqv\ndescription: ataqv function of a corresponding ataqv tool\nkeywords:\n - ATAC-seq\n - qc\n - ataqv\ntool"
},
{
"path": "modules/nf-core/ataqv/mkarv/main.nf",
"chars": 895,
"preview": "process ATAQV_MKARV {\n label 'process_medium'\n\n conda 'bioconda::ataqv=1.3.1'\n container \"${ workflow.container"
},
{
"path": "modules/nf-core/ataqv/mkarv/meta.yml",
"chars": 1039,
"preview": "name: \"ataqv_mkarv\"\ndescription: mkarv function of a corresponding ataqv tool\nkeywords:\n - ataqv\n - ATAC-seq\n - qc\n "
},
{
"path": "modules/nf-core/bowtie2/align/main.nf",
"chars": 3538,
"preview": "process BOWTIE2_ALIGN {\n tag \"$meta.id\"\n label \"process_high\"\n\n conda \"bioconda::bowtie2=2.4.4 bioconda::samtoo"
},
{
"path": "modules/nf-core/bowtie2/align/meta.yml",
"chars": 1854,
"preview": "name: bowtie2_align\ndescription: Align reads to a reference genome using bowtie2\nkeywords:\n - align\n - map\n - fasta\n "
},
{
"path": "modules/nf-core/bowtie2/build/main.nf",
"chars": 1249,
"preview": "process BOWTIE2_BUILD {\n tag \"$fasta\"\n label 'process_high'\n\n conda \"bioconda::bowtie2=2.4.4\"\n container \"${"
},
{
"path": "modules/nf-core/bowtie2/build/meta.yml",
"chars": 1148,
"preview": "name: bowtie2_build\ndescription: Builds bowtie index for reference genome\nkeywords:\n - build\n - index\n - fasta\n - ge"
},
{
"path": "modules/nf-core/bwa/index/main.nf",
"chars": 1199,
"preview": "process BWA_INDEX {\n tag \"$fasta\"\n label 'process_single'\n\n conda \"bioconda::bwa=0.7.17\"\n container \"${ work"
},
{
"path": "modules/nf-core/bwa/index/meta.yml",
"chars": 1103,
"preview": "name: bwa_index\ndescription: Create BWA index for reference genome\nkeywords:\n - index\n - fasta\n - genome\n - referenc"
},
{
"path": "modules/nf-core/bwa/mem/main.nf",
"chars": 1460,
"preview": "process BWA_MEM {\n tag \"$meta.id\"\n label 'process_high'\n\n conda \"bioconda::bwa=0.7.17 bioconda::samtools=1.16.1"
},
{
"path": "modules/nf-core/bwa/mem/meta.yml",
"chars": 1500,
"preview": "name: bwa_mem\ndescription: Performs fastq alignment to a fasta reference using BWA\nkeywords:\n - mem\n - bwa\n - alignme"
},
{
"path": "modules/nf-core/chromap/chromap/main.nf",
"chars": 3198,
"preview": "process CHROMAP_CHROMAP {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::chromap=0.2.4 bioconda::sa"
},
{
"path": "modules/nf-core/chromap/chromap/meta.yml",
"chars": 2327,
"preview": "name: chromap_chromap\ndescription: |\n Performs preprocessing and alignment of chromatin fastq files to\n fasta referenc"
},
{
"path": "modules/nf-core/chromap/index/main.nf",
"chars": 916,
"preview": "process CHROMAP_INDEX {\n tag \"$fasta\"\n label 'process_medium'\n\n conda \"bioconda::chromap=0.2.4\"\n container \""
},
{
"path": "modules/nf-core/chromap/index/meta.yml",
"chars": 1048,
"preview": "name: chromap_index\ndescription: Indexes a fasta reference genome ready for chromatin profiling.\nkeywords:\n - index\n -"
},
{
"path": "modules/nf-core/custom/dumpsoftwareversions/main.nf",
"chars": 785,
"preview": "process CUSTOM_DUMPSOFTWAREVERSIONS {\n label 'process_single'\n\n // Requires `pyyaml` which does not have a dedicat"
},
{
"path": "modules/nf-core/custom/dumpsoftwareversions/meta.yml",
"chars": 1094,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json\nname: "
},
{
"path": "modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py",
"chars": 3375,
"preview": "#!/usr/bin/env python\n\n\n\"\"\"Provide functions to merge multiple versions.yml files.\"\"\"\n\n\nimport yaml\nimport platform\nfrom"
},
{
"path": "modules/nf-core/custom/getchromsizes/main.nf",
"chars": 1265,
"preview": "process CUSTOM_GETCHROMSIZES {\n tag \"$fasta\"\n label 'process_single'\n\n conda \"bioconda::samtools=1.16.1\"\n co"
},
{
"path": "modules/nf-core/custom/getchromsizes/meta.yml",
"chars": 1352,
"preview": "name: custom_getchromsizes\ndescription: Generates a FASTA file of chromosome sizes and a fasta index file\nkeywords:\n - "
},
{
"path": "modules/nf-core/deeptools/computematrix/main.nf",
"chars": 1184,
"preview": "process DEEPTOOLS_COMPUTEMATRIX {\n tag \"$meta.id\"\n label 'process_high'\n\n conda \"bioconda::deeptools=3.5.1\"\n "
},
{
"path": "modules/nf-core/deeptools/computematrix/meta.yml",
"chars": 1550,
"preview": "name: deeptools_computematrix\ndescription: calculates scores per genome regions for other deeptools plotting utilities\nk"
},
{
"path": "modules/nf-core/deeptools/plotfingerprint/main.nf",
"chars": 1425,
"preview": "process DEEPTOOLS_PLOTFINGERPRINT {\n tag \"$meta.id\"\n label 'process_high'\n\n conda \"bioconda::deeptools=3.5.1\"\n "
},
{
"path": "modules/nf-core/deeptools/plotfingerprint/meta.yml",
"chars": 1556,
"preview": "name: deeptools_plotfingerprint\ndescription: plots cumulative reads coverages by BAM file\nkeywords:\n - plot\n - fingerp"
},
{
"path": "modules/nf-core/deeptools/plotheatmap/main.nf",
"chars": 1054,
"preview": "process DEEPTOOLS_PLOTHEATMAP {\n tag \"$meta.id\"\n label 'process_low'\n\n conda \"bioconda::deeptools=3.5.1\"\n co"
},
{
"path": "modules/nf-core/deeptools/plotheatmap/meta.yml",
"chars": 1411,
"preview": "name: deeptools_plotheatmap\ndescription: plots values produced by deeptools_computematrix as a heatmap\nkeywords:\n - plo"
},
{
"path": "modules/nf-core/deeptools/plotprofile/main.nf",
"chars": 1048,
"preview": "process DEEPTOOLS_PLOTPROFILE {\n tag \"$meta.id\"\n label 'process_low'\n\n conda \"bioconda::deeptools=3.5.1\"\n co"
},
{
"path": "modules/nf-core/deeptools/plotprofile/meta.yml",
"chars": 1416,
"preview": "name: deeptools_plotprofile\ndescription: plots values produced by deeptools_computematrix as a profile plot\nkeywords:\n "
},
{
"path": "modules/nf-core/fastqc/main.nf",
"chars": 1790,
"preview": "process FASTQC {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::fastqc=0.11.9\"\n container \"${ wo"
},
{
"path": "modules/nf-core/fastqc/meta.yml",
"chars": 1480,
"preview": "name: fastqc\ndescription: Run FastQC on sequenced reads\nkeywords:\n - quality control\n - qc\n - adapters\n - fastq\ntool"
},
{
"path": "modules/nf-core/gffread/main.nf",
"chars": 830,
"preview": "process GFFREAD {\n tag \"$gff\"\n label 'process_low'\n\n conda \"bioconda::gffread=0.12.1\"\n container \"${ workflo"
},
{
"path": "modules/nf-core/gffread/meta.yml",
"chars": 980,
"preview": "name: gffread\ndescription: Validate, filter, convert and perform various other operations on GFF files\nkeywords:\n - gff"
},
{
"path": "modules/nf-core/gunzip/main.nf",
"chars": 1313,
"preview": "process GUNZIP {\n tag \"$archive\"\n label 'process_single'\n\n conda \"conda-forge::sed=4.7\"\n container \"${ workf"
},
{
"path": "modules/nf-core/gunzip/meta.yml",
"chars": 905,
"preview": "name: gunzip\ndescription: Compresses and decompresses files.\nkeywords:\n - gunzip\n - compression\n - decompression\ntool"
},
{
"path": "modules/nf-core/homer/annotatepeaks/main.nf",
"chars": 1347,
"preview": "process HOMER_ANNOTATEPEAKS {\n tag \"$meta.id\"\n label 'process_medium'\n\n // WARN: Version information not provid"
},
{
"path": "modules/nf-core/homer/annotatepeaks/meta.yml",
"chars": 1425,
"preview": "name: homer_annotatepeaks\ndescription: Annotate peaks with HOMER suite\nkeywords:\n - annotations\n - peaks\n - bed\ntools"
},
{
"path": "modules/nf-core/khmer/uniquekmers/main.nf",
"chars": 1004,
"preview": "process KHMER_UNIQUEKMERS {\n tag \"$fasta\"\n label 'process_low'\n\n conda \"bioconda::khmer=3.0.0a3\"\n container "
},
{
"path": "modules/nf-core/khmer/uniquekmers/meta.yml",
"chars": 1067,
"preview": "name: \"khmer_uniquekmers\"\ndescription: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more"
},
{
"path": "modules/nf-core/macs2/callpeak/main.nf",
"chars": 1720,
"preview": "process MACS2_CALLPEAK {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::macs2=2.2.7.1\"\n containe"
},
{
"path": "modules/nf-core/macs2/callpeak/meta.yml",
"chars": 1744,
"preview": "name: macs2_callpeak\ndescription: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments\nkeywords"
},
{
"path": "modules/nf-core/picard/collectmultiplemetrics/main.nf",
"chars": 2498,
"preview": "process PICARD_COLLECTMULTIPLEMETRICS {\n tag \"$meta.id\"\n label 'process_single'\n\n conda \"bioconda::picard=3.0.0"
},
{
"path": "modules/nf-core/picard/collectmultiplemetrics/meta.yml",
"chars": 1809,
"preview": "name: picard_collectmultiplemetrics\ndescription: Collect multiple metrics from a BAM file\nkeywords:\n - alignment\n - me"
},
{
"path": "modules/nf-core/picard/markduplicates/main.nf",
"chars": 1938,
"preview": "process PICARD_MARKDUPLICATES {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::picard=3.0.0\"\n co"
},
{
"path": "modules/nf-core/picard/markduplicates/meta.yml",
"chars": 1913,
"preview": "name: picard_markduplicates\ndescription: Locate and tag duplicate reads in a BAM file\nkeywords:\n - markduplicates\n - p"
},
{
"path": "modules/nf-core/picard/mergesamfiles/main.nf",
"chars": 1692,
"preview": "process PICARD_MERGESAMFILES {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::picard=3.0.0\"\n con"
},
{
"path": "modules/nf-core/picard/mergesamfiles/meta.yml",
"chars": 1078,
"preview": "name: picard_mergesamfiles\ndescription: Merges multiple BAM files into a single file\nkeywords:\n - merge\n - alignment\n "
},
{
"path": "modules/nf-core/preseq/lcextrap/main.nf",
"chars": 1163,
"preview": "process PRESEQ_LCEXTRAP {\n tag \"$meta.id\"\n label 'process_single'\n label 'error_ignore'\n\n conda \"bioconda::p"
},
{
"path": "modules/nf-core/preseq/lcextrap/meta.yml",
"chars": 1327,
"preview": "name: preseq_lcextrap\ndescription: Software for predicting library complexity and genome coverage in high-throughput seq"
},
{
"path": "modules/nf-core/samtools/flagstat/main.nf",
"chars": 993,
"preview": "process SAMTOOLS_FLAGSTAT {\n tag \"$meta.id\"\n label 'process_single'\n\n conda \"bioconda::samtools=1.17\"\n conta"
},
{
"path": "modules/nf-core/samtools/flagstat/meta.yml",
"chars": 1400,
"preview": "name: samtools_flagstat\ndescription: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type\nkeywords:"
},
{
"path": "modules/nf-core/samtools/idxstats/main.nf",
"chars": 996,
"preview": "process SAMTOOLS_IDXSTATS {\n tag \"$meta.id\"\n label 'process_single'\n\n conda \"bioconda::samtools=1.17\"\n conta"
},
{
"path": "modules/nf-core/samtools/idxstats/meta.yml",
"chars": 1402,
"preview": "name: samtools_idxstats\ndescription: Reports alignment summary statistics for a BAM/CRAM/SAM file\nkeywords:\n - stats\n "
},
{
"path": "modules/nf-core/samtools/index/main.nf",
"chars": 1307,
"preview": "process SAMTOOLS_INDEX {\n tag \"$meta.id\"\n label 'process_low'\n\n conda \"bioconda::samtools=1.17\"\n container \""
},
{
"path": "modules/nf-core/samtools/index/meta.yml",
"chars": 1418,
"preview": "name: samtools_index\ndescription: Index SAM/BAM/CRAM file\nkeywords:\n - index\n - bam\n - sam\n - cram\ntools:\n - samtoo"
},
{
"path": "modules/nf-core/samtools/sort/main.nf",
"chars": 1432,
"preview": "process SAMTOOLS_SORT {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::samtools=1.17\"\n container"
},
{
"path": "modules/nf-core/samtools/sort/meta.yml",
"chars": 1304,
"preview": "name: samtools_sort\ndescription: Sort SAM/BAM/CRAM file\nkeywords:\n - sort\n - bam\n - sam\n - cram\ntools:\n - samtools:"
},
{
"path": "modules/nf-core/samtools/stats/main.nf",
"chars": 1380,
"preview": "process SAMTOOLS_STATS {\n tag \"$meta.id\"\n label 'process_single'\n\n conda \"bioconda::samtools=1.17\"\n containe"
},
{
"path": "modules/nf-core/samtools/stats/meta.yml",
"chars": 1679,
"preview": "name: samtools_stats\ndescription: Produces comprehensive statistics from SAM/BAM/CRAM file\nkeywords:\n - statistics\n - "
},
{
"path": "modules/nf-core/subread/featurecounts/main.nf",
"chars": 1411,
"preview": "process SUBREAD_FEATURECOUNTS {\n tag \"$meta.id\"\n label 'process_medium'\n\n conda \"bioconda::subread=2.0.1\"\n c"
},
{
"path": "modules/nf-core/subread/featurecounts/meta.yml",
"chars": 1571,
"preview": "name: subread_featurecounts\ndescription: Count reads that map to genomic features\nkeywords:\n - counts\n - fasta\n - gen"
},
{
"path": "modules/nf-core/trimgalore/main.nf",
"chars": 2912,
"preview": "process TRIMGALORE {\n tag \"$meta.id\"\n label 'process_high'\n\n conda \"bioconda::trim-galore=0.6.7\"\n container "
},
{
"path": "modules/nf-core/trimgalore/meta.yml",
"chars": 1969,
"preview": "name: trimgalore\ndescription: Trim FastQ files using Trim Galore!\nkeywords:\n - trimming\n - adapters\n - sequencing ada"
},
{
"path": "modules/nf-core/ucsc/bedgraphtobigwig/main.nf",
"chars": 1556,
"preview": "process UCSC_BEDGRAPHTOBIGWIG {\n tag \"$meta.id\"\n label 'process_single'\n\n // WARN: Version information not prov"
},
{
"path": "modules/nf-core/ucsc/bedgraphtobigwig/meta.yml",
"chars": 1149,
"preview": "name: ucsc_bedgraphtobigwig\ndescription: Convert a bedGraph file to bigWig format.\nkeywords:\n - bedgraph\n - bigwig\n -"
},
{
"path": "modules/nf-core/umitools/extract/main.nf",
"chars": 1696,
"preview": "process UMITOOLS_EXTRACT {\n tag \"$meta.id\"\n label \"process_single\"\n label \"process_long\"\n\n conda \"bioconda::"
},
{
"path": "modules/nf-core/umitools/extract/meta.yml",
"chars": 1383,
"preview": "name: umitools_extract\ndescription: Extracts UMI barcode from a read and add it to the read name, leaving any sample bar"
},
{
"path": "modules/nf-core/untar/main.nf",
"chars": 1881,
"preview": "process UNTAR {\n tag \"$archive\"\n label 'process_single'\n\n conda \"conda-forge::sed=4.7 bioconda::grep=3.4 conda-"
},
{
"path": "modules/nf-core/untar/meta.yml",
"chars": 949,
"preview": "name: untar\ndescription: Extract files.\nkeywords:\n - untar\n - uncompress\n - extract\ntools:\n - untar:\n descripti"
},
{
"path": "modules.json",
"chars": 10557,
"preview": "{\n \"name\": \"nf-core/atacseq\",\n \"homePage\": \"https://github.com/nf-core/atacseq\",\n \"repos\": {\n \"https://g"
},
{
"path": "nextflow.config",
"chars": 11439,
"preview": "/*\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n nf-core/atacseq Nextflow"
},
{
"path": "nextflow_schema.json",
"chars": 39814,
"preview": "{\n \"$schema\": \"http://json-schema.org/draft-07/schema\",\n \"$id\": \"https://raw.githubusercontent.com/nf-core/atacseq"
},
{
"path": "pyproject.toml",
"chars": 359,
"preview": "# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.\n# Should be kept the "
},
{
"path": "subworkflows/local/align_star.nf",
"chars": 2272,
"preview": "/*\n * Map reads, sort, index BAM file and run samtools stats, flagstat and idxstats\n */\n\ninclude { STAR_ALIGN "
},
{
"path": "subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc.nf",
"chars": 1254,
"preview": "\n//\n// Convert BAM to normalised bigWig via bedGraph using BEDTools and UCSC\n//\n\ninclude { BEDTOOLS_GENOMECOV } from "
},
{
"path": "subworkflows/local/bam_filter_bamtools.nf",
"chars": 3393,
"preview": "include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main'\ninclude { SAMTOOLS_INDEX } "
},
{
"path": "subworkflows/local/bam_peaks_call_qc_annotate_macs2_homer.nf",
"chars": 5990,
"preview": "//\n// Call peaks with MACS2, annotate with HOMER and perform downstream QC\n//\n\ninclude { MACS2_CALLPEAK } from"
},
{
"path": "subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf",
"chars": 5487,
"preview": "//\n// Call consensus peaks with BEDTools and custom scripts, annotate with HOMER, quantify with featureCounts and QC wit"
},
{
"path": "subworkflows/local/bigwig_plot_deeptools.nf",
"chars": 2780,
"preview": "\n//\n// Create coverage matrices, plot coverage profiles and heatmap with deepTools\n//\n\ninclude { DEEPTOOLS_PLOTPROFILE }"
},
{
"path": "subworkflows/local/input_check.nf",
"chars": 1850,
"preview": "//\n// Check input samplesheet and get read channels\n//\n\ninclude { SAMPLESHEET_CHECK } from '../../modules/local/samplesh"
},
{
"path": "subworkflows/local/prepare_genome.nf",
"chars": 9701,
"preview": "//\n// Uncompress and prepare reference genome files\n//\n\ninclude {\n GUNZIP as GUNZIP_FASTA\n GUNZIP as GUNZIP_GTF\n "
},
{
"path": "subworkflows/nf-core/bam_markduplicates_picard/main.nf",
"chars": 2032,
"preview": "//\n// Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats\n//\n\ninclude { PICARD_MARKDUPLI"
},
{
"path": "subworkflows/nf-core/bam_markduplicates_picard/meta.yml",
"chars": 1635,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json\nn"
},
{
"path": "subworkflows/nf-core/bam_sort_stats_samtools/main.nf",
"chars": 1818,
"preview": "//\n// Sort, index BAM file and run samtools stats, flagstat and idxstats\n//\n\ninclude { SAMTOOLS_SORT } from '../../"
},
{
"path": "subworkflows/nf-core/bam_sort_stats_samtools/meta.yml",
"chars": 1718,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json\nn"
},
{
"path": "subworkflows/nf-core/bam_stats_samtools/main.nf",
"chars": 1179,
"preview": "//\n// Run SAMtools stats, flagstat and idxstats\n//\n\ninclude { SAMTOOLS_STATS } from '../../../modules/nf-core/samtool"
},
{
"path": "subworkflows/nf-core/bam_stats_samtools/meta.yml",
"chars": 1159,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json\nn"
},
{
"path": "subworkflows/nf-core/fastq_align_bowtie2/main.nf",
"chars": 1869,
"preview": "//\n// Alignment with Bowtie2\n//\n\ninclude { BOWTIE2_ALIGN } from '../../../modules/nf-core/bowtie2/align/main'\n"
},
{
"path": "subworkflows/nf-core/fastq_align_bowtie2/meta.yml",
"chars": 1781,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json\nn"
},
{
"path": "subworkflows/nf-core/fastq_align_bwa/main.nf",
"chars": 1645,
"preview": "//\n// Alignment with BWA\n//\n\ninclude { BWA_MEM } from '../../../modules/nf-core/bwa/mem/main'\ninclude { "
},
{
"path": "subworkflows/nf-core/fastq_align_bwa/meta.yml",
"chars": 2023,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json\nn"
},
{
"path": "subworkflows/nf-core/fastq_align_chromap/main.nf",
"chars": 1841,
"preview": "/*\n * Map reads, sort, index BAM file and run samtools stats, flagstat and idxstats\n */\n\ninclude { CHROMAP_CHROMAP "
},
{
"path": "subworkflows/nf-core/fastq_align_chromap/meta.yml",
"chars": 2617,
"preview": "# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json\nn"
},
{
"path": "subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf",
"chars": 4520,
"preview": "//\n// Read QC, UMI extraction and trimming\n//\n\ninclude { FASTQC } from '../../../modules/nf-core/fastqc/main'\n"
}
]
// ... and 4 more files (download for full content)
About this extraction
This page contains the full source code of the nf-core/atacseq GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 204 files (1.0 MB), approximately 340.7k tokens, and a symbol index with 15 extracted functions, classes, methods, constants, and types. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.
Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.