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maxulysseFriederikeHanssentdanhornThomas
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Release 3.5.1 (#1799)
<!-- # nf-core/sarek pull request Many thanks for contributing to nf-core/sarek! 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/sarek/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/sarek/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,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). --------- Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: Friederike Hanssen <[email protected]> Co-authored-by: tdanhorn <[email protected]> Co-authored-by: Thomas <[email protected]>
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‎.github/workflows/cloudtest.yml

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@@ -81,13 +81,24 @@ jobs:
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if: github.repository == 'nf-core/sarek' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
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runs-on: ubuntu-latest
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steps:
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- uses: octokit/[email protected]
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- name: Get PR reviews
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uses: octokit/[email protected]
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if: github.event_name != 'workflow_dispatch'
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id: check_approvals
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continue-on-error: true
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with:
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
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route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- id: test_variables
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- name: Check for approvals
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if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
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run: |
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echo "No review approvals found. At least 2 approvals are required to run this action automatically."
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exit 1
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- name: Check for enough approvals (>=2)
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id: test_variables
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if: github.event_name != 'workflow_dispatch'
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run: |
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JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
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}
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profiles: ${{ matrix.profile }}
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- uses: actions/upload-artifact@v3
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name: Save Logs
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if: success() || failure()
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- uses: actions/upload-artifact@v4
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with:
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name: tower-${{ matrix.profile }}-log
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎CHANGELOG.md

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@@ -5,6 +5,37 @@ All notable changes to this project will be documented in this file.
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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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## [3.5.1](https://github.com/nf-core/sarek/releases/tag/3.5.1) - Akkatjåkkå
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Akkatjåkkå is another glacier.
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### Added
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- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev
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### Changed
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- [1767](https://github.com/nf-core/sarek/pull/1767) - Bump nf-schema version to 2.2.1
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- [1777](https://github.com/nf-core/sarek/pull/1777) - Merge intervals for WES in GATK GenomicsDBImport
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- [1798](https://github.com/nf-core/sarek/pull/1798) - Prepare release 3.5.1
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### Fixed
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- [1797](https://github.com/nf-core/sarek/pull/1797) - Use `file-path-pattern` over `file-path` to hanlde glob for `known_indels` and `known_indels_tbi` to fix [1785](https://github.com/nf-core/sarek/issues/1785)
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- [1802](https://github.com/nf-core/sarek/pull/1802) - Update GHA for full_test tests
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### Removed
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### Dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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### Parameters
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| Params | Status |
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| ------ | ------ |
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## [3.5.0](https://github.com/nf-core/sarek/releases/tag/3.5.0) - Áhkájiegna
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A set of connecting glaciers.

‎assets/multiqc_config.yml

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custom_logo_title: "nf-core/sarek"
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.5.0" target="_blank">nf-core/sarek</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/sarek/3.5.0/docs/output" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.5.1"
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target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to
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interpret these results, please see the <a href="https://nf-co.re/sarek/3.5.1/docs/output"
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target="_blank">documentation</a>.
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report_section_order:
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"nf-core-sarek-methods-description":
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order: -1000
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name: "FastP (Read preprocessing)"
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- picard:
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name: "GATK4 MarkDuplicates"
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info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)."
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info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity
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(with --use_gatk_spark)."
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- samtools:
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name: "Samtools Flagstat"
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- mosdepth:
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pattern: "^.*.(md|recal).mosdepth.(global|region).dist"
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module: mosdepth
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sample_names_replace_regex: True
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sample_names_replace_regex: true
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sample_names_replace:
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"\\.[0-9]{4}$": ".md" # should match ".0001" but only at the end of strings for module Markduplicates/EstimateLibraryComplexity
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module: picard

‎conf/modules/joint_germline.config

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process {
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withName: 'GATK4_GENOMICSDBIMPORT' {
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ext.args = { '--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
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ext.args = { params.wes ?
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'--merge-input-intervals --genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' :
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'--genomicsdb-shared-posixfs-optimizations true --bypass-feature-reader' }
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ext.prefix = { "${meta.intervals_name}.joint" }
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publishDir = [
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enabled: false

‎nextflow.config

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}
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// Set bash options
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process.shell = """\
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bash
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set -e # Exit if a tool returns a non-zero status/exit code
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set -u # Treat unset variables and parameters as an error
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set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
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set -C # No clobber - prevent output redirection from overwriting files.
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"""
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process.shell = [
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"bash",
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"-C", // No clobber - prevent output redirection from overwriting files.
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"-e", // Exit if a tool returns a non-zero status/exit code
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"-u", // Treat unset variables and parameters as an error
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"-o", // Returns the status of the last command to exit..
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"pipefail" // ..with a non-zero status or zero if all successfully execute
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]
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// Disable process selector warnings by default. Use debug profile to enable warnings.
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nextflow.enable.configProcessNamesValidation = false
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description = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
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mainScript = 'main.nf'
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nextflowVersion = '!>=24.04.2'
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version = '3.5.0'
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version = '3.5.1'
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doi = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
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}
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// Nextflow plugins
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plugins {
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id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
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id 'nf-schema@2.2.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
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id '[email protected]' // Provenance reports for pipeline runs
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}
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‎nextflow_schema.json

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"known_indels": {
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"type": "string",
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"fa_icon": "fas fa-copy",
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"format": "file-path",
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"format": "file-path-pattern",
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"exists": true,
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"mimetype": "text/plain",
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"description": "Path to known indels file.",
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"known_indels_tbi": {
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"type": "string",
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"fa_icon": "fas fa-copy",
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"format": "file-path",
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"format": "file-path-pattern",
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"exists": true,
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"mimetype": "text/plain",
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"description": "Path to known indels file index.",

‎tests/aligner-bwa-mem.nf.test.snap

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"samtools": 1.21
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},
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"Workflow": {
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"nf-core/sarek": "v3.5.0"
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"nf-core/sarek": "v3.5.1"
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}
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},
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[
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{
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"Workflow": {
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"nf-core/sarek": "v3.5.0"
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"nf-core/sarek": "v3.5.1"
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}
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},
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[

‎tests/aligner-bwa-mem2.nf.test.snap

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{
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"Workflow": {
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"nf-core/sarek": "v3.5.0"
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"nf-core/sarek": "v3.5.1"
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}
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},
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"samtools": 1.21
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},
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"Workflow": {
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"nf-core/sarek": "v3.5.0"
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"nf-core/sarek": "v3.5.1"
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‎tests/aligner-dragmap.nf.test.snap

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"Workflow": {
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"nf-core/sarek": "v3.5.1"
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"Workflow": {
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"nf-core/sarek": "v3.5.0"
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"nf-core/sarek": "v3.5.1"
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‎tests/alignment_from_everything.nf.test.snap

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"vcftools": "0.1.16"
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},
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"Workflow": {
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"nf-core/sarek": "v3.5.0"
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"nf-core/sarek": "v3.5.1"
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}
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[

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