Name		Name	Last commit message	Last commit date
Latest commit History 1,044 Commits
.github		.github
abra2_2.17		abra2_2.17
abra2_2.19		abra2_2.19
abra2_2.22		abra2_2.22
access_utils/0.1.1		access_utils/0.1.1
alfred_0.1.17		alfred_0.1.17
athena/1.4.2		athena/1.4.2
bcftools_1.15.1		bcftools_1.15.1
bcftools_1.6		bcftools_1.6
bedtools_genomecov_v2.28.0_cv2		bedtools_genomecov_v2.28.0_cv2
bedtools_merge_v2.28.0_cv2		bedtools_merge_v2.28.0_cv2
bedtools_sortBed_v2.28.0_cv2		bedtools_sortBed_v2.28.0_cv2
biometrics_extract		biometrics_extract
biometrics_genotype		biometrics_genotype
biometrics_major		biometrics_major
biometrics_minor		biometrics_minor
biometrics_sexmismatch		biometrics_sexmismatch
bwa_mem_0.7.12		bwa_mem_0.7.12
bwa_mem_0.7.17		bwa_mem_0.7.17
bwa_mem_0.7.5a		bwa_mem_0.7.5a
cci_utils/0.3.1		cci_utils/0.3.1
cwl_commandlinetools		cwl_commandlinetools
delly_0.9.1		delly_0.9.1
delly_1.0.3		delly_1.0.3
disambiguate_1.0.0		disambiguate_1.0.0
docs		docs
expression_tools		expression_tools
facets_1.5.6		facets_1.5.6
fastp_0.20.1		fastp_0.20.1
fgbio_call_duplex_consensus_reads_1.2.0		fgbio_call_duplex_consensus_reads_1.2.0
fgbio_collect_duplex_seq_metrics_1.2.0		fgbio_collect_duplex_seq_metrics_1.2.0
fgbio_fastq_to_bam_1.2.0		fgbio_fastq_to_bam_1.2.0
fgbio_filter_consensus_reads_1.2.0		fgbio_filter_consensus_reads_1.2.0
fgbio_group_reads_by_umi_1.2.0		fgbio_group_reads_by_umi_1.2.0
fgbio_postprocessing_simplex_filter_0.1.8		fgbio_postprocessing_simplex_filter_0.1.8
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_apply_bqsr_4.1.8.1		gatk_apply_bqsr_4.1.8.1
gatk_base_recalibrator_4.1.0.0		gatk_base_recalibrator_4.1.0.0
gatk_base_recalibrator_4.1.8.1		gatk_base_recalibrator_4.1.8.1
gatk_collect_alignment_summary_metrics_4.1.8.0		gatk_collect_alignment_summary_metrics_4.1.8.0
gatk_collect_hs_metrics_4.1.8.0		gatk_collect_hs_metrics_4.1.8.0
gatk_collect_insert_size_metrics_4.1.8.0		gatk_collect_insert_size_metrics_4.1.8.0
gatk_downsamplesam_4.1.8.1		gatk_downsamplesam_4.1.8.1
gatk_mark_duplicates_4.1.0.0		gatk_mark_duplicates_4.1.0.0
gatk_mean_quality_by_cycle		gatk_mean_quality_by_cycle
gatk_merge_bam_alignment_4.1.8.0		gatk_merge_bam_alignment_4.1.8.0
gatk_merge_sam_files_4.1.8.0		gatk_merge_sam_files_4.1.8.0
gatk_revert_sam		gatk_revert_sam
gatk_sam_to_fastq_4.1.8.0		gatk_sam_to_fastq_4.1.8.0
getbasecountsmultisample/1.2.5		getbasecountsmultisample/1.2.5
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
mosdepth_0.3.3		mosdepth_0.3.3
msisensor_0.2		msisensor_0.2
msisensor_0.6		msisensor_0.6
multiqc		multiqc
mutect2_4.1.0.0		mutect2_4.1.0.0
mutect_1.1.5		mutect_1.1.5
octopus/0.7.4		octopus/0.7.4
oncokb_annotator_3.2.2		oncokb_annotator_3.2.2
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_add_or_replace_read_groups_4.1.8.1		picard_add_or_replace_read_groups_4.1.8.1
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_fix_mate_information_2.9.0		picard_fix_mate_information_2.9.0
picard_fix_mate_information_4.1.8.1		picard_fix_mate_information_4.1.8.1
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
picard_mark_duplicates_2.9.0		picard_mark_duplicates_2.9.0
picard_mark_duplicates_4.1.8.1		picard_mark_duplicates_4.1.8.1
postprocessing_variant_calls		postprocessing_variant_calls
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
sequence_qc		sequence_qc
snp-pileup_0.1.1		snp-pileup_0.1.1
snpsift_annotate_5.0		snpsift_annotate_5.0
tests		tests
trim_galore_0.6.2		trim_galore_0.6.2
utilities_ubuntu_18.04		utilities_ubuntu_18.04
vardictjava		vardictjava
vcf2maf_1.6.17		vcf2maf_1.6.17
vcf2maf_1.6.21		vcf2maf_1.6.21
waltz_count_reads_3.1.1		waltz_count_reads_3.1.1
waltz_pileupmatrices_3.1.1		waltz_pileupmatrices_3.1.1

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

Command-line tools built by CCI

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 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

License

msk-access/cwl-commandlinetools

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