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Merge pull request #449 from JoseEspinosa/merging-template-3.2.0
Merging-template-3.2.0
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‎.github/workflows/ci.yml‎

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steps:
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- name: Check out pipeline code
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uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
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with:
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fetch-depth: 0
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- name: Set up Nextflow
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uses: nf-core/setup-nextflow@v2

‎.github/workflows/download_pipeline.yml‎

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REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
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REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
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REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
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steps:
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- name: Get the repository name and current branch
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id: get_repo_properties
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run: |
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echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
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echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
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echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
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download:
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runs-on: ubuntu-latest
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needs: configure
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steps:
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v2
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python -m pip install --upgrade pip
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pip install git+https://github.com/nf-core/tools.git@dev
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- name: Get the repository name and current branch set as environment variable
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id: get_repo_properties
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run: |
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echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
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echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
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echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
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- name: Make a cache directory for the container images
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run: |
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mkdir -p ./singularity_container_images
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download:
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runs-on: ubuntu-latest
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needs: configure
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steps:
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- name: Download the pipeline
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env:
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NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
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- name: Inspect download
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run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
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- name: Inspect container images
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run: tree ./singularity_container_images | tee ./container_initial
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- name: Count the downloaded number of container images
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id: count_initial
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run: |
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final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
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difference=$((final_count - initial_count))
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echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
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tree ./singularity_container_images
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tree ./singularity_container_images > ./container_afterwards
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diff ./container_initial ./container_afterwards
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exit 1
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else
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echo "The pipeline can be downloaded successfully!"

‎.github/workflows/linting_comment.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Download lint results
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uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
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uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
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with:
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workflow: linting.yml
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workflow_conclusion: completed

‎.github/workflows/release-announcements.yml‎

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${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
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send-tweet:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: pip install tweepy==4.14.0
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- name: Send tweet
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shell: python
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run: |
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import os
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import tweepy
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client = tweepy.Client(
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access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
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access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
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consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
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consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
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)
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tweet = os.getenv("TWEET")
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client.create_tweet(text=tweet)
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env:
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TWEET: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
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TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
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TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
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TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
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bsky-post:
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runs-on: ubuntu-latest
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steps:

‎.nf-core.yml‎

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- config_defaults:
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- params.bamtools_filter_se_config
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- params.bamtools_filter_pe_config
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nf_core_version: 3.1.1
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nf_core_version: 3.2.0
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repository_type: pipeline
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template:
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author: Espinosa-Carrasco J, Patel H, Wang C, Ewels P

‎.pre-commit-config.yaml‎

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- [email protected]
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- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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rev: "3.0.3"
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rev: "3.1.2"
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hooks:
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- id: editorconfig-checker
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alias: ec

‎CHANGELOG.md‎

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- [[PR #434](https://github.com/nf-core/chipseq/pull/434)] - Prevent pipeline fails from erroneous param validation when igenomes is used.
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- [[#432](https://github.com/nf-core/chipseq/issues/432)] - Fix `GFFREAD` call to have the two expected input channels.
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- [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
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- Updated pipeline template to [nf-core/tools 3.2.0](https://github.com/nf-core/tools/releases/tag/3.2.0)
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### Parameters
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‎README.md‎

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<source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-chipseq_logo_dark.png">
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<img alt="nf-core/chipseq" src="docs/images/nf-core-chipseq_logo_light.png">
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</picture>
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</h1>[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/ci.yml)
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</h1>
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[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/ci.yml)
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[![GitHub Actions Linting Status](https://github.com/nf-core/chipseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3240506-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3240506)
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[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
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## Usage
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> [!NOTE]
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> 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.
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> 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.
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To run on your data, prepare a tab-separated samplesheet with your input data. Please follow the [documentation on samplesheets](https://nf-co.re/chipseq/usage#samplesheet-input) for more details. An example samplesheet for running the pipeline looks as follows:
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‎modules.json‎

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},
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"fastqc": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
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"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
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},
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"gffread": {
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
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"git_sha": "f0719ae309075ae4a291533883847c3f7c441dad",
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"installed_by": ["modules"]
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},
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"phantompeakqualtools": {

‎modules/nf-core/fastqc/main.nf‎

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