Explore Workflows

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

Graph Name Retrieved From View
workflow graph sorter.cwl

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/sorter.cwl

Branch/Commit ID: 5b866e480fb557cf53d619a22068c73548e337d5
workflow graph count-lines5-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd
workflow graph Cellranger Reanalyze

Cellranger Reanalyze

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
workflow graph conflict-wf.cwl#collision

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc

Packed ID: collision
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl

Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9
workflow graph transform_pack.cwl#fastq_clean_pe.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/transform_pack.cwl

Branch/Commit ID: 0c1a40ea1efb1656644ccec0b7abe659539340e7

Packed ID: fastq_clean_pe.cwl
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 9144d08fa7f4e852498761481dceab477167fa65
workflow graph sec-wf-out.cwl

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: fd6e054510e2bb65eed4069a3a88013d7ecbb99c
workflow graph Generate genome indices for STAR & bowtie

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: 17a4a68b20e0af656e09714c1f39fe761b518686
workflow graph transform.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/dnaseq/transform.cwl

Branch/Commit ID: f34d3963b33e0a379338cb3cb75b0016f012bf2c