Explore Workflows

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

Graph Name Retrieved From View
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: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb
workflow graph copy_outputs.cwl

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

Path: workflows/copy_outputs.cwl

Branch/Commit ID: 4034144f39a9428307e82efe1f812c1d37c79de5
workflow graph transcriptome_cleanup

This workflow detect and remove vector, duplicate and contamination from a transcriptome fasta file

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Annotation/transcriptome-cleanup.cwl

Branch/Commit ID: de6380d83f9209e95559e66cf64ded3bf0e410ea
workflow graph extract_capture_kit_http.cwl

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

Path: workflows/bamfastq_align/extract_capture_kit_http.cwl

Branch/Commit ID: 20a901f44c9fb0e6f4ee3c40ec33fa4b1c8ef005
workflow graph qc_workflow_wo_waltz.cwl

This workflow is intended to be used to test the QC module, without having to run the long waltz step

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow_wo_waltz.cwl

Branch/Commit ID: 7061957d31023d922501fba61310b2d82de61c15
workflow graph env-wf3.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/env-wf3.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: cwltool/schemas/v1.0/v1.0/revsort.cwl

Branch/Commit ID: 280a852e74aec08cf79687e8004e17b1ab464534
workflow graph harmonization_novoalign_multi_readgroup.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/harmonization_novoalign_multi_readgroup.cwl

Branch/Commit ID: 7eb6b9f75db20866611a3bc55bee28746e84c1b6
workflow graph apolloServer-createOrganism-workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: apolloServer-createOrganism-workflow.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph count-lines6-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 7bfd77118cdc80dd7150115dd7a1a7ee6046f6fe