MSK-ACCESS sub-workflows

description
Central location for storing common workflow language based sub-workflows for building msk-access workflows

Features

Create sub-workflows in common workflow language to generate msk-access parent workflow.

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

MSKCC - Members of Center for Molecular Oncology
MSKCC - Memebers of Department of Molecular Pathology
Cookiecutter: https://github.com/audreyr/cookiecutter
audreyr/cookiecutter-pypackage: https://github.com/audreyr/cookiecutter-pypackage

Name		Name	Last commit message	Last commit date
Latest commit History 667 Commits
.github/workflows		.github/workflows
alignment		alignment
athena_report		athena_report
bam_qc_stats		bam_qc_stats
base_quality_recalibration		base_quality_recalibration
command_line_tools @ b8c66ac		command_line_tools @ b8c66ac
cwl_subworkflows		cwl_subworkflows
docs		docs
fgbio_separate_bams		fgbio_separate_bams
gbcms_genotyping		gbcms_genotyping
indel_realignment		indel_realignment
qc_collapsed_bam		qc_collapsed_bam
qc_duplex_bam		qc_duplex_bam
qc_simplex_bam		qc_simplex_bam
qc_uncollapsed_bam		qc_uncollapsed_bam
tests		tests
vardict_workflow		vardict_workflow
variant_annotation		variant_annotation
variant_postprocessing		variant_postprocessing
.editorconfig		.editorconfig
.gitbook.yaml		.gitbook.yaml
.gitignore		.gitignore
.gitmodules		.gitmodules
.travis.yml		.travis.yml
LICENSE		LICENSE
MANIFEST.in		MANIFEST.in
Makefile		Makefile
README.md		README.md
requirements.txt		requirements.txt
requirements_p2.7.txt		requirements_p2.7.txt
setup.cfg		setup.cfg
setup.py		setup.py
tox.ini		tox.ini