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Dev -> master for 3.14.0 release#1156

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drpatelh merged 89 commits intomasternf-core/rnaseq:masterfrom devnf-core/rnaseq:devCopy head branch name to clipboardJan 8, 2024

+644-241

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Commits on Nov 21, 2023

• Bump versions for work on 3.14.0 milestone

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• [automated] Fix linting with Prettier

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• Merge pull request #1129 from nf-core/bump_release_dev

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Commits on Nov 27, 2023

• Update cloud_tests_full to action-tower-launch-v2

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• Update cloud_tests_small to action-tower-launch v2

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Commits on Nov 28, 2023

• Make output directory path instead of file?

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• Run on self-hosted

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• Revert self-hosted

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• Add revision parameter to action

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• Update CHANGELOG.md

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• Add PR to CHANGELOG

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Commits on Dec 4, 2023

• MultiQC dupradar custom plot: specify plot_type explicitly

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Commits on Dec 8, 2023

• Update FastQC and UMItools modules

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• Update CHANGELOG

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• Merge pull request #1135 from nf-core/update-action-tower-launch-to-v2

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• Merge branch 'dev' into dev

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• Update modules with stderr updated

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• Update Changelog

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• Fix formatting

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• Update channel names from bam_rseqc subworkflow update

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• Update bam_rseqc subworkflow again

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• Update CHANGELOG.md

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• Merge pull request #1138 from mahesh-panchal/dev

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Commits on Dec 11, 2023

• Merge pull request #1137 from vladsavelyev/multiqc-dupradar-plottype

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Commits on Dec 19, 2023

• Template update for nf-core/tools version 2.11

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Commits on Dec 20, 2023

• Template update for nf-core/tools version 2.11.1

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Commits on Dec 21, 2023

• Try more flexible requires for genome

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• Prettier

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Commits on Dec 22, 2023

• Provide interface to pseudoaligner kmer length

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• Update CHANGELOG

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• Fix param name

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• Temporarily disable latest testing

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• Merge branch 'dev' into nf-core-template-merge-2.11

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• Fix module

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• Don't put STDERR in versions string for UMITOOLS_PREPAREFORRSEM

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• Merge pull request #1141 from nf-core/nf-core-template-merge-2.11

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• Merge branch 'dev' into interface_to_kmer

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• add missing changelog entry

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• Merge branch 'dev' into genome_fasta_required

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Commits on Jan 3, 2024

• Update CHANGELOG

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• Revert "Update FastQC and UMItools modules"

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• Merge pull request #1148 from nf-core/revert-1138-dev

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• Patch modules to fix #1103

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• Merge branch 'dev' into interface_to_kmer

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• Update ci.yml - fix test matrix

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• Reinstate non-schema fasta checking

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• Update CHANGELOG

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• Update CHANGELOG.md

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• Merge branch 'dev' into genome_fasta_required

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• Update CHANGELOG.md

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• Merge pull request #1149 from drpatelh/updates

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• Merge branch 'dev' into genome_fasta_required

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• Merge branch 'dev' into interface_to_kmer

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• Merge pull request #1144 from nf-core/interface_to_kmer

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• Merge branch 'dev' into genome_fasta_required

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• Be more flexible on attribute values in GTFs

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• Update tx2gene.py

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• Update CHANGELOG.md

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• Update CHANGELOG.md

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• Merge pull request #1143 from nf-core/genome_fasta_required

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• Update CHANGELOG.md

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• Merge branch 'dev' into flexible_tx2gene

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• Merge pull request #1150 from nf-core/flexible_tx2gene

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Commits on Jan 4, 2024

• fix to #1150

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• Update CHANGELOG.md

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• Merge pull request #1151 from nf-core/fix_gtf_flexibility

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• Bump qualimap version to 2.3

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• Bump rseqc version to 5.0.3

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• [skip ci] Patch qualimap and rseqc modules

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• Update CHANGELOG

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• Merge pull request #1152 from drpatelh/fixes

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• Disable additional multiqc versions section

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• Defer strand inference until after trimming and filtering

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• [skip ci] bump versions

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• Fix conditional publishing to avoid empty dirs

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• [skip ci] update changelog

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• Merge branch 'dev' into prerelease_3.14.0_fixes

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Commits on Jan 5, 2024

• Apply suggestions from code review

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• Merge pull request #1154 from nf-core/prerelease_3.14.0_fixes

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• [skip ci] Add slash to outdir for cloud tests to fix Azure validation issue

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• Update CHANGELOG

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• Merge pull request #1157 from drpatelh/fixes

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Commits on Jan 7, 2024

• Bump MultiQC version from 1.17 -> 1.19

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• [skip ci] Bump CHANGELOG

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• Update CHANGELOG

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• Fix prettier

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• Merge pull request #1159 from drpatelh/fixes

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Commits on Jan 8, 2024

• Final prerelease fixes

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• Merge pull request #1160 from drpatelh/fixes

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