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Try matthias' fix to download#1439

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pinin4fjords wants to merge 101 commits intomasternf-core/rnaseq:masterfrom try_sc_download_fixnf-core/rnaseq:try_sc_download_fixCopy head branch name to clipboard

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Commits on Oct 16, 2024

• Merge pull request #1417 from nf-core/master

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• Bump versions back to 3.17.0 after release

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• Update CHANGELOG

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• Prettier

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• Merge pull request #1418 from nf-core/postrelease_3.16.1

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Commits on Oct 17, 2024

• appy changes for ARM

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• Merge branch 'arm_3.16.1' into dev

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• Fix up config

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• Reset environment ymls

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• Reset main.nfs with software changes only

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• Link sw configs to arm profile

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• Add process block

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• note pins

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• Remove conda overrides that were having no impact

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Commits on Oct 18, 2024

• Use different RSEQC pin

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• update BEDGRAPHTOBIGWIG pin

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• Fix annotation

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• Don't think we need the RSEQC pin

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• correct ucsc

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• Merge pull request #1 from pinin4fjords/sw_to_conf

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• Triage arm deps

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• Non-igenomes STAR can use the latest star

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• remove rogue comment

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Commits on Oct 21, 2024

• update arm conf

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• Bump lots of modules so that conda versions have arm builds

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• Update prepare_genome snaps

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• Update align_star snaps

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• Update quantify_rsem snaps

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• [skip ci] First batch of pipeline test updates

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• [skip ci] Update subworkflow snaps due to patch on module

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• [skip ci] bump remove_ribo_rna snaps

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• Merge branch 'bump_modules_for_arm' of https://github.com/nf-core/rnaseq into bump_modules_for_arm

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• [skip ci] Update snaps for --pseudo_aligner salmon --skip_qc --skip_alignment

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• [skip ci] update star_rsem pipeline snaps

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• Merge branch 'bump_modules_for_arm' of https://github.com/nf-core/rnaseq into bump_modules_for_arm

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• [skip ci] update pipeline tests for skip_qc

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• Merge branch 'bump_modules_for_arm' of https://github.com/nf-core/rnaseq into bump_modules_for_arm

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• update skip_trimming snaps

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• update changelog

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  787ab18

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• Revert hisat diff

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• remove excess newlines

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• Merge pull request #1422 from nf-core/bump_modules_for_arm

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• Bump star modules

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• Update option for new STAR

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  f99460d

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• Fix up pipeline tests

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• Fix local star swf to match star

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• update changelog

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Commits on Oct 22, 2024

• Merge pull request #1423 from nf-core/bump_star

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• patch sortmerna to 4.3.7 in seqera channel pending a functional verison appearing in conda-forge

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• Update changelog

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• fix sortmerna tests for order

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• update a relevant pipeline test

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• Merge pull request #1424 from nf-core/bump_sortmerna

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• Cut out module redundant software overrides

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• Merge pull request #2 from pinin4fjords/triage_arm

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• Merge pull request #1414 from pabloaledo/dev

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• Merge branch 'dev' into arm_3.16.1

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• Add frozen ARM builds

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• Container directives for conda overrides

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• Temporary Trimgalore override, singularity fixes for rsem processes

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  8e14711

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• update docs

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• Fix argument conflict between STAR versions

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• Fix config error

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• Correction to star rsem

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• Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1

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• Refine config setup

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  4f8de94

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• Bump trimgalore module

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• Fix up ARM profile for updated trim-galore

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Commits on Oct 23, 2024

• Apply suggestions from code review

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• Apply suggestions from code review

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• Add notes for kraken2/ braken

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• Update docs

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• prettier

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• lint fix

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• [skip ci] Reorg ARM bits

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• Update arm.config

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• Fix syntax error

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• Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1

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• revert trimgalore tweak to appease linter

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• Update pipeline-level tests

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• Merge branch 'arm_3.16.1' of https://github.com/nf-core/rnaseq into arm_3.16.1

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• Update CHANGELOG

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• Merge branch 'arm_3.16.1' of github.com:nf-core/rnaseq into arm_3.16.1

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• Merge pull request #1425 from nf-core/arm_3.16.1

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• Bump versions

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• update changelog

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• Merge pull request #1432 from nf-core/prerelease_3.17.0

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• update CHANGELOG

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• update and patch modules

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• Merge pull request #1434 from maxulysse/default_registry_no_exception

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• update CHANGELOG

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• fix CI

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• Merge branch 'dev' into CHANGELOG

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• update CHANGELOG

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• fix GHA

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• revert GHA

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• revert CHANGELOG

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• update CHANGELOG

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• remove conda from matrix

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• Merge pull request #1437 from maxulysse/CHANGELOG

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• Update download_pipeline.yml

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