MSK-ACCESS command-line tools

description
Central location for storing common workflow language based command line tools for building msk-access workflows

MSK-ACCESS command-line tools

Free software: Apache Software License 2.0

Documentation: https://msk-access.gitbook.io/command-line-tools-cwl/

Features

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

Installation

Clone the repository:

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

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

Credits

CMO ACCESS Informatics Team
This package was created with Cookiecutter_ and the audreyr/cookiecutter-pypackage_ project template.
- 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 252 Commits
.github		.github
abra2_2.17		abra2_2.17
abra2_2.19		abra2_2.19
alfred_0.1.17		alfred_0.1.17
bedtools_genomecov_v2.28.0_cv2		bedtools_genomecov_v2.28.0_cv2
bedtools_merge_v2.28.0_cv2		bedtools_merge_v2.28.0_cv2
bwa_mem_0.7.12		bwa_mem_0.7.12
bwa_mem_0.7.5a		bwa_mem_0.7.5a
cwl_commandlinetools		cwl_commandlinetools
disambiguate_1.0.0		disambiguate_1.0.0
docs		docs
facets_1.5.6		facets_1.5.6
gatk_ApplyBQSR_4.1.2.0		gatk_ApplyBQSR_4.1.2.0
gatk_BaseRecalibrator_4.1.2.0		gatk_BaseRecalibrator_4.1.2.0
gatk_apply_bqsr_4.1.0.0		gatk_apply_bqsr_4.1.0.0
gatk_base_recalibrator_4.1.0.0		gatk_base_recalibrator_4.1.0.0
gatk_mark_duplicates_4.1.0.0		gatk_mark_duplicates_4.1.0.0
manta_1.5.1		manta_1.5.1
marianas_collapsing_first_pass_1.8.1		marianas_collapsing_first_pass_1.8.1
marianas_collapsing_second_pass_1.8.1		marianas_collapsing_second_pass_1.8.1
marianas_process_loop_umi_1.8.1		marianas_process_loop_umi_1.8.1
marianas_separate_bams_1.8.1		marianas_separate_bams_1.8.1
merge_fastq_0.1.7		merge_fastq_0.1.7
msisensor_0.2		msisensor_0.2
msisensor_0.6		msisensor_0.6
mutect2_4.1.0.0		mutect2_4.1.0.0
mutect_1.1.5		mutect_1.1.5
picard_add_or_replace_read_groups_1.96		picard_add_or_replace_read_groups_1.96
picard_add_or_replace_read_groups_2.21.2		picard_add_or_replace_read_groups_2.21.2
picard_collect_alignment_summary_metrics_2.21.2		picard_collect_alignment_summary_metrics_2.21.2
picard_collect_alignment_summary_metrics_2.8.1		picard_collect_alignment_summary_metrics_2.8.1
picard_collectmultiplemetric_2.21.2		picard_collectmultiplemetric_2.21.2
picard_collectmultiplemetric_2.8.1		picard_collectmultiplemetric_2.8.1
picard_fix_mate_information_1.96		picard_fix_mate_information_1.96
picard_fix_mate_information_2.21.2		picard_fix_mate_information_2.21.2
picard_hsmetrics_2.21.2		picard_hsmetrics_2.21.2
picard_hsmetrics_2.8.1		picard_hsmetrics_2.8.1
picard_mark_duplicates_1.96		picard_mark_duplicates_1.96
picard_mark_duplicates_2.21.2		picard_mark_duplicates_2.21.2
picard_mark_duplicates_2.8.1		picard_mark_duplicates_2.8.1
samtools-merge_1.9		samtools-merge_1.9
samtools_sort_1.3.1		samtools_sort_1.3.1
samtools_view_1.3.1		samtools_view_1.3.1
scatterintervals_4.1.0.0		scatterintervals_4.1.0.0
snp-pileup_0.1.1		snp-pileup_0.1.1
tests		tests
trim_galore_0.6.2		trim_galore_0.6.2
utilities_ubuntu_18.04		utilities_ubuntu_18.04
waltz_count_reads_3.1.1		waltz_count_reads_3.1.1
waltz_pileupmatrices_3.1.1		waltz_pileupmatrices_3.1.1
.editorconfig		.editorconfig
.gitbook.yaml		.gitbook.yaml
.gitignore		.gitignore
.travis.yml		.travis.yml
LICENSE		LICENSE
MANIFEST.in		MANIFEST.in
Makefile		Makefile
README.md		README.md
__init__.py		__init__.py
requirements.txt		requirements.txt
requirements_p2.7.txt		requirements_p2.7.txt
setup.cfg		setup.cfg
setup.py		setup.py
tox.ini		tox.ini

License

mskcc/cwl-commandlinetools

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