Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines18-wf.cwl

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

Path: tests/count-lines18-wf.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph 1st-workflow.cwl

https://github.com/golharam/cwl-graph-generate.git

Path: test/1st-workflow.cwl

Branch/Commit ID: e39bdf429fa96a645d0995f153af22cac7a1bc38
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: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: dc2c019c1aa24cc01b451a0f048cf94a35f163c4
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph cond-wf-012.cwl

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

Path: tests/conditionals/cond-wf-012.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph Pairwise genomic regions intersection

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

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

Path: workflows/peak-intersect.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph scatterfail.cwl

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: 4bb5329997cb84562a40733b5c2f55600b1a741a
workflow graph record-in-secondaryFiles-missing-wf.cwl

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

Path: tests/record-in-secondaryFiles-missing-wf.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph lane_map_and_stats.cwl

https://github.com/cancerit/cgpRna.git

Path: cwls/tools/lane_map_and_stats.cwl

Branch/Commit ID: 6d77a181dc077de726bc78a19d30c22399797312