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Merge pull request #36 from nf-core/nf-core-template-merge-3.2.0
Important! Template update for nf-core/tools v3.2.0
2 parents 0ac6a3f + 719abaa commit e693f8c

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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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nextflow_config:
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- config_defaults:
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- params.ribo_database_manifest
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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: Avani Bhojwani and Timothy Little

‎.pre-commit-config.yaml‎

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- prettier@3.2.5
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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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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v1.2.0 - [2025-01-13]
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## v1.2.0 - [2025-02-03]
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- [PR #25](https://github.com/nf-core/denovotranscript/pull/25) - Bump version to 1.2.0dev
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- [PR #27](https://github.com/nf-core/denovotranscript/pull/27) - Update spades resources and usage instructions
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- [PR #30](https://github.com/nf-core/denovotranscript/pull/30) - Fix ch_transcripts and ch_pubids for AWS
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- [PR #32](https://github.com/nf-core/denovotranscript/pull/32) - Fix transrate dependencies issue
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- [PR #33](https://github.com/nf-core/denovotranscript/pull/33) - Bump version to 1.2.0
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- [PR #36](https://github.com/nf-core/denovotranscript/pull/36) - Template update for nf-core/tools v3.2.0
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## v1.1.0 - [2024-11-28]
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‎assets/multiqc_config.yml‎

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/denovotranscript/releases/tag/1.2.0"
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target="_blank">nf-core/denovotranscript</a> analysis pipeline. For information
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about how to interpret these results, please see the <a href="https://nf-co.re/denovotranscript/1.2.0/docs/output"
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target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/denovotranscript/releases/tag/1.2.0" target="_blank">nf-core/denovotranscript</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/denovotranscript/1.2.0/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-denovotranscript-methods-description":
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order: -1000

‎modules.json‎

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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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"salmon/index": {

‎modules/nf-core/fastqc/main.nf‎

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