Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph count-lines4-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph step-valuefrom3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom3-wf.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c
workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: 17bae57a1f00f5c6db8f3a82d86262f12b8153cf
workflow graph Nested workflow example

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 1b5633876aabd4cb57ef3f1fe91c853f3ee82e46
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca
workflow graph Single-Cell RNA-Seq Filtering Analysis

Single-Cell RNA-Seq Filtering Analysis Removes low-quality cells from the outputs of the “Cell Ranger Count (RNA)”, “Cell Ranger Count (RNA+VDJ)”, and “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines. The results of this workflow are used in the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline.

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

Path: workflows/sc-rna-filter.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 4ea5956bb97ea2eb6de124bc9b6a6a81a14fd2e7
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 20d664eff23e59aa57908345bfdb1ceeab3438f2
workflow graph collect_pair_files.cwl

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

Path: modules/pair/collect_pair_files.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6
workflow graph BWA index pipeline

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