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Release 4.2.0#358

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ggabernet merged 132 commits intomasternf-core/airrflow:masterfrom devnf-core/airrflow:devCopy head branch name to clipboardDec 11, 2024

+15,828-1,427

Commits

Commits on Mar 21, 2024

• first steps & sc run

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Commits on Mar 25, 2024

• input change

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Commits on Apr 10, 2024

• stage before pull

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• Merge remote-tracking branch 'origin/master' into dev

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Commits on Apr 11, 2024

• merged most recent airrflow version

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• barcode airr test

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Commits on May 6, 2024

• dev update

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• Merge branch 'master' of https://github.com/mapo9/airrflow into trust4

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Commits on May 7, 2024

• skip presto reporting which doesnt happen when trust4 is used

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Commits on May 8, 2024

• linting

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• fastp before trust4

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Commits on May 10, 2024

• fastp before trust4

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Commits on May 16, 2024

• bulk and sc rnaseq input

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• bulk rnaseq test workflow

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• sc rnaseq tests

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• docs

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• linting & prettier

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• trailing whitespace

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• trailing whitespace

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Commits on May 21, 2024

• bugfix

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• trailing whitespace

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• view statement removed

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Commits on May 23, 2024

• incorporating review comments

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• fix test

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• removed view statement

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Commits on May 28, 2024

• Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow into trust4

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• generate reference fasta

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• channel in wrong subworkflow

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• generate trust4 reference

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Commits on May 29, 2024

• Merge branch 'dev' of https://github.com/nf-core/airrflow into trust4

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Commits on May 30, 2024

• Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow into trust4

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Commits on May 31, 2024

• merge dev

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• add param skip alignment filter

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Commits on Jun 3, 2024

• add 'config_profile_url' default

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Commits on Jun 5, 2024

• trust4 nf-core module

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Commits on Jul 14, 2024

• also store unproductive seqs

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• make unproductive optional

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Commits on Jul 17, 2024

• fix cregion primer annotation

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• improve docs

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• Merge branch 'trust4' of https://github.com/mapo9/airrflow into trust4

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• fix prettier

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• add locus selection to rnaseq workflow

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• fix issue with merge_UMI

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• Merge pull request #334 from mapo9/trust4

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Commits on Jul 22, 2024

• Merge branch 'nf-core:dev' into dev

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Commits on Aug 19, 2024

• Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow into dev

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• Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow into dev

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• simplify maskprimers score

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• do not save presto intermediate fastq

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Commits on Aug 20, 2024

• add maskprimers extract option

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• update changelog

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• update modules config

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• implement pairseq for clustersets

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• update modules.config

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Commits on Aug 21, 2024

• add buildconsensus extract pairseq extract

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• Merge branch 'clustersets' into dev

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• update changelog

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• update changelog

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Commits on Aug 23, 2024

• parametrize clustersets

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Commits on Aug 28, 2024

• update clustersets umi

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• update modules config

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Commits on Aug 30, 2024

• remove vprimer and cprimer requirement for maskprimers_extract

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Commits on Sep 3, 2024

• do not stage log to results dir

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Commits on Sep 4, 2024

• makedb partial for mouse TR

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Commits on Sep 5, 2024

• improve TRUST4 docs

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Commits on Sep 15, 2024

• fix maskprimers test noumi

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• fix maskprimers sansumi

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• fix assemblepairs sansumi

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• maskprimers align sansumi

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Commits on Sep 16, 2024

• maskprimers sansumi assemble

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Commits on Sep 22, 2024

• fix suffix maskprimers algin

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• Merge branch 'clustersets' into dev

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Commits on Sep 23, 2024

• fix log maskprimers align

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Commits on Sep 26, 2024

• bump cellranger version

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• bumped actions/upload-artifact to v4 to circumvent deprecated version error in test

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Commits on Sep 27, 2024

• implement maskprimers align umi

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• fix linting

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• fix ci workflow

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Commits on Sep 30, 2024

• Merge pull request #347 from mapo9/bump_cellranger

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Commits on Oct 1, 2024

• fix parselogs merge df

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Commits on Oct 8, 2024

• Template update for nf-core/tools version 3.0.0

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Commits on Oct 9, 2024

• Template update for nf-core/tools version 3.0.1

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Commits on Oct 11, 2024

• Template update for nf-core/tools version 3.0.2

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Commits on Oct 14, 2024

• update schema

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• Merge branch 'TEMPLATE' of https://github.com/nf-core/airrflow into merge-template-updates

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• add resourceLimits to test configs

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• fix issues template update

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• Merge branch 'dev' into dev

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• fix linting

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• fix linting

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• Merge branch 'dev' of https://github.com/ggabernet/nf-core-airrflow into dev

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  fdb06ce

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• fix linting

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• fix CI issues

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• fix ci issues

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• update test requirements

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• presto collapseq n=0

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Commits on Oct 19, 2024

• fix trust4 prepare reference

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• collapseseq sansumi

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Commits on Oct 21, 2024

• update barcode_read to cell_barcode_read

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• allow age to be int

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Commits on Oct 22, 2024

• update trust4 module

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  6629693

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• fix trust4 reference

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• fix precommit

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• increase time

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• fix test profile

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• fix trust4 reference

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• fix maskprimers align race

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• try debugging

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• desperate...

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Commits on Oct 25, 2024

• Merge pull request #344 from ggabernet/dev

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Commits on Nov 3, 2024

• fix docs nebnext mouse

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Commits on Nov 5, 2024

• update enchantr docker container

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• change name to C_REGION

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Commits on Nov 25, 2024

• rm unnecessary isotype_column param

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Commits on Nov 26, 2024

• update changelog

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• bump versions for release

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  de349f1

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• update changelog

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• Fix linting

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• update changelog

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  9c0e84b

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• bump enchantr version

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• Merge pull request #357 from ggabernet/dev

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• rm conda from ci tests

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• apply reviewer suggestions

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Commits on Nov 27, 2024

• Merge pull request #359 from ggabernet/dev

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• Update .nf-core.yml

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Commits on Nov 28, 2024

• metro map including trust4

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Commits on Dec 9, 2024

• Merge branch 'dev' of github.com:ggabernet/nf-core-airrflow into dev

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Commits on Dec 10, 2024

• update metro map

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• update workflow overview

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• Merge branch 'dev' of github.com:nf-core/airrflow into dev

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• Merge pull request #360 from ggabernet/dev

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• fix ci setup nextfow

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