Explore Workflows

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

Graph Name Retrieved From View
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq_alignment.cwl

Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/gathered_somatic_exome.cwl

Branch/Commit ID: f21b6c6f70f01d0fe08193684060161107f0bf59
workflow graph Replace legacy AML Trio Assay

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

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0
workflow graph schemadef-wf.cwl

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

Path: v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: 17695244222b0301b37cb749fe4a8d89622cd1ad
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: ef266744578e2dcbce57c110c6fa3b9eee91e316
workflow graph js-expr-req-wf.cwl#wf

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

Path: tests/js-expr-req-wf.cwl

Branch/Commit ID: 86c46cb397de029e4c91f02cca40fa2b54d22f37

Packed ID: wf
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: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph metrics-flow.cwl

Run metrics workflow

 https://github.com/sentieon/sentieon-cwl.git

Path: stage/metrics-flow.cwl

Branch/Commit ID: d20382adfe7285cb517a25d95d2bcb7586546e23