Command Line Tools (CWL)
develop
develop1.0.0
develop
develop1.0.0
  • MSK-ACCESS command-line tools
  • ABRA2
    • v2.17
    • v2.22
  • access_utils
    • 0.1.1
  • bcftools
    • bcftools bgzip v1.15.1
    • bcftools concat v1.15.1
    • bcftools norm v1.15.1
    • bcftools sort v1.15.1
    • bcftools tabix v1.15.1
  • Bedtools
    • genomecov v2.28.0_cv2
    • merge v2.28.0_cv2
    • sortbed v2.28.0_cv2
  • Biometrics
    • extract
    • minor
    • major
    • genotype
    • sexmismatch
  • Delly
    • delly call 0.9.1
    • delly call 1.0.3
  • Disambiguate
    • v1.0.0
  • Fastp
    • 0.20.1
    • 0.24.0
  • Fgbio
    • CallDuplexConsensusReads v1.2.0
    • CollectDuplexSeqMetrics v1.2.0
    • GroupReadsByUmi v1.2.0
    • FastqToBam v1.2.0
    • FilterConsensusReads v1.2.0
    • simplex_filter v0.1.8
  • GATK
    • ApplyBQSR v4.1.2.0
    • ApplyBQSR v4.1.8.1
    • BaseRecalibrator v4.1.2.0
    • BaseRecalibrator v4.1.8.1
    • MergeBamAlignment v4.1.8.0
    • MergeSamFiles v4.1.8.0
    • SamToFastq v4.1.8.0
  • GetBaseCountsMultiSample
    • 1.2.5
  • Manta
    • Manta v1.5.1
  • Marianas
    • Collapsing First Pass v1.8.1
    • Collapsing Second Pass v1.8.1
    • Process Loop UMI v1.8.1
    • Seprate BAMs v1.8.1
  • MultiQC
    • MultiQC v1.10.1.7
    • MultiQC v1.12
  • MuTect
    • MuTect 1.1.5
  • Merge Fastq
    • v0.1.7
  • Mosdepth
    • 0.3.3
  • Octopus
    • v0.7.4
  • Oncokb_annotator
    • v3.2.2
  • Picard Tools
    • AddOrReplaceReadGroups v1.96
    • AddOrReplaceReadGroups v2.21.2
    • AddOrReplaceReadGroups v4.1.8.1
    • CollectAlignmentSummaryMetrics v2.8.1
    • CollectAlignmentSummaryMetrics v2.21.2
    • CollectMultipleMetrics v2.8.1
    • CollectMultipleMetrics v2.21.2
    • FixMateInformation v1.96
    • FixMateInformation v2.21.2
    • FixMateInformation v4.1.8.1
    • HSmetrics v2.8.1
    • HSmetrics v2.21.2
    • MarkDuplicates v1.96
    • MarkDuplicates v2.8.1
    • MarkDuplicates v2.21.2
    • MarkDuplicates v4.1.8.1
  • Postprocessing variant calls
    • vardict_filter_case-control 0.1.5
    • vardict_filter_single-sample 0.1.5
    • maf_annotated_by_bed_0.2.2
    • maf_annotated_by_tsv_0.2.3
    • maf_filter_cmoch_0.2.3
    • maf_tag_cmoch_0.2.3
    • maf_annotated_by_bed_0.2.3
  • sequence_qc
    • v0.2.4
  • SnpSift
    • v5.0
  • Trim Galore
    • v0.6.2
  • Ubuntu utilites
    • v18.04
  • VarDictJava
    • v1.8.2
  • VCF2MAF
    • 1.6.21
  • Waltz
    • CountReads v3.1.1
    • PileupMetrics v3.1.1
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MSK-ACCESS command-line tools

Central location for storing common workflow language based command line tools for building workflows

NextABRA2

Last updated 2 years ago

  • Free software: Apache Software License 2.0

  • Documentation:

Features

Create command line tools in common workflow language to generate workflows.

Installation

Clone the repository:

git clone --depth 50 https://github.com/msk-access/cwl-commandlinetools.git

Follow the README in repsective tool folder for execution of the tool.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

  • Cookiecutter:

  • audreyr/cookiecutter-pypackage:

https://msk-access.gitbook.io/command-line-tools-cwl/
https://github.com/audreyr/cookiecutter
https://github.com/audreyr/cookiecutter-pypackage