Explore Workflows

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/mut2.cwl

Branch/Commit ID: 20d664eff23e59aa57908345bfdb1ceeab3438f2

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/collect_pair_files.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

https://github.com/datirium/workflows.git

Path: workflows/bwa-index.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20

Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

https://github.com/Barski-lab/workflows.git

Path: workflows/heatmap.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/immuno.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/js_output_workflow.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 3034168d652bfa930ba09af20e473a4564a8010d

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/steplevel-resreq.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7