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Commits on Feb 29, 2024

• Update MQC container (nf-core#5006)

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  matthdsm

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  mashehu

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Commits on Feb 28, 2024

• remove params.outdir from modules and subworfklows tests (nf-core#5007)

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  maxulysse

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• Make BBSPLIT indexing behave itself (nf-core#5005)

  pinin4fjords

  authored
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Commits on Feb 27, 2024

• Update amrfinderplus to version 3.12.8 (nf-core#5004)

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  jasmezz

  and

  CarsonJM

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  8f4a5d5

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• Add new submodule MMseqs/taxonomy (nf-core#4980)

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  Darcy220606

  authored
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• gatk4/applybqsr : Using modules_testdata_base_path instead of test_data in nf-test (nf-core#4995)

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  asp8200

  authored
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Commits on Feb 26, 2024

• Fix sortmerna indexing (nf-core#5003)

  pinin4fjords

  authored
  8aa7040

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• Fix testdata path in three gatk4 modules (nf-core#5000)

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  asp8200

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  194fca8

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• gatk4/baserecalibrator : Using modules_testdata_base_path instead of test_data in nf-test (nf-core#4997)

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  asp8200

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• cat/cat : Using modules_testdata_base_path instead of test_data in nf-test (nf-core#4990)

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  asp8200

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• dragmap/align : modules_testdata_base_path instead of test_data in nf-test (nf-core#4993)

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  asp8200

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• Update data path for all rseqc modules at once (nf-core#4994)

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  maxulysse

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• Allow sortmerna to operate in indexing-only mode (nf-core#4998)

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  pinin4fjords

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  maxulysse

  authored
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• update data path for modules custom/tx2gene (nf-core#4991)

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  maxulysse

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• bwa/mem : Using modules_testdata_base_path instead of test_data in nf-test (nf-core#4988)

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  asp8200

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• bwa/index : modules_testdata_base_path instead of test_data in nf-test (nf-core#4987)

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  asp8200

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• Update paths in subread/featurecounts (nf-core#4977)

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  adamrtalbot

  and

  maxulysse

  authored
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• update data path for modules custom/catadditionalfasta (nf-core#4989)

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  maxulysse

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• Added stub and nf-test for samblaster (nf-core#4985)

  GallVp

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Commits on Feb 25, 2024

• Added a draft for LAI (nf-core#4771)

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  GallVp

  authored
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Commits on Feb 24, 2024

• Reorder rnaseq preprocessing, fix minor issues, test sortmerna (nf-core#4982)

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  pinin4fjords

  authored
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• Update rgi/main to 6.0.3 (nf-core#4933)

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  jasmezz

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Commits on Feb 23, 2024

• Update paths in summarizedexperiment (nf-core#4978)

  adamrtalbot

  authored
  874dace

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• Update gfaffix to 0.1.5b (nf-core#4971)

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  heuermh

  authored
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• Updates to gnu sort module to include nf-test (nf-core#4950)

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  DLBPointon

  authored
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• Smoove/call stub & nf-test (nf-core#4974)

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  nvnieuwk

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Commits on Feb 22, 2024

• Added parallel version of ltrharvest (nf-core#4968)

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  GallVp

  authored
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• Kraken2/add module (nf-core#4703)

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• add missing cryptography dependency to CI (nf-core#4973)

  mashehu

  authored
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• fix tiny bug in gawk module (nf-core#4972)

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  MariekeVromman

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• bump gatk4 modules (nf-core#4900)

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  3 peopleauthored
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• tentative fix for gatk broad image issues (nf-core#4969)

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  matthdsm

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Commits on Feb 21, 2024

• Fix conda cat version to match container in cat/fastq (nf-core#4965)

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  pinin4fjords

  authored
  0997b47

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• Stop UMItools prepare-for-rsem command writing to the input file (nf-core#4966)

  pinin4fjords

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• Added to the config test data file a path to new test data from test-datasets (nf-core#4946)

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  Salome-Brunon

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  maxulysse

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