Code

Tooling for long-read-pipelines#326

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Merged

rhpvorderman merged 33 commits intodevelopbiowdl/tasks:developfrom SASC-2572biowdl/tasks:SASC-2572Copy head branch name to clipboardFeb 5, 2025

+335-23

Commits

Commits on Nov 8, 2024

• Update minimap2 task to output sorted BAM

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  53d5083

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• Add a flag for namesorting

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  77506d8

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• Add clair3 task

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  e78cfa0

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• Add sequali and update multiqc to a version that supports it

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  0d84d67

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• Fix womtool validation errors

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  2728422

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• Fix runtime issues

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  01ff19c

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• Include all contigs by default for clair3

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  a488618

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• Work from a model tar file

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Commits on Nov 11, 2024

• Set includeAlCtgs to false

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  8fa4811

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Commits on Nov 12, 2024

• Increase memory

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  98d9e2c

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Commits on Dec 13, 2024

• Add a readgroup flag to minimap2

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  a6eec0e

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Commits on Dec 17, 2024

• Add -o pipefail

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Commits on Jan 8, 2025

• Allow copying of comments from fastq

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  42ca869

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Commits on Jan 10, 2025

• Allow minimap2 to process uBAM

  rhpvorderman

  committed
  7240b17

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• Allow sample name to set

  rhpvorderman

  committed
  c7c1b5b

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• Proper numshards to deepvariant and update it to latest version

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Commits on Jan 29, 2025

• Add modkit pileup

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  a5dca2e

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• Update modkit

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  085fc5d

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• Add memory to modkit

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  3540b4a

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• Add missing backslash

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  bc17987

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• Set rather high defaults for time and memory for modkit

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  c69c5cb

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• Upgrade sequali memory

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  beec409

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Commits on Feb 3, 2025

• Add modkit flags

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  a87956e

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• Capture multiple output files

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  730a8a7

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Commits on Feb 4, 2025

• Update documentation for new tasks

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  ed50e2d

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Commits on Feb 5, 2025

• Update changelog

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  113d4c5

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• Merge branch 'develop' into SASC-2572

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  8d469a1

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• Indent clair3 command

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  a01b54a

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• Merge branch 'SASC-2572' of https://github.com/biowdl/tasks into SASC-2572

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  e24a067

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• More realistic resource requirements for modkit

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  b409ca9

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• More specific bed file naming

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  committed
  bdab5a4

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• Correct file extension for modkit

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  committed
  c79ebd4

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• Correct whitespacing

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  DavyCats

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  1580aae

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