Explore Workflows

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

Graph Name Retrieved From View
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: f100a34cf4ffb0e81c468dc10005068a53ec0f75
workflow graph pdx-pl.cwl

https://github.com/WEHI-ResearchComputing/pdx-genome.git

Path: src/pdx-pl.cwl

Branch/Commit ID: 4bf9858ea46ed81165357e1b15575c581cb5c181
workflow graph metrics.cwl

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

Path: workflows/mirnaseq/metrics.cwl

Branch/Commit ID: 52e1db2baf586cef97c4cea396f459201d8a74d3
workflow graph TOPMed_RNA-seq

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL) Pipeline steps: 1. Align RNA-seq reads with [STAR v2.5.3a](https://github.com/alexdobin/STAR). 2. Run [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). 2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6](https://github.com/samtools/samtools/releases) index. 3. Transcript quantification with [RSEM 1.3.0](https://deweylab.github.io/RSEM/) 4. Gene quantification and quality control with [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc)

https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git

Path: workflow/rnaseq_pipeline_fastq.cwl

Branch/Commit ID: 6f1cbe68f7c8b7ae5d3ed00ac7f912a8265ea50b
workflow graph sum-wf.cwl

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

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

Branch/Commit ID: 2b295864bc81b59b0698af8076474465afcf48d8
workflow graph wgs alignment with qc

https://github.com/genome/cancer-genomics-workflow.git

Path: wgs_alignment.cwl

Branch/Commit ID: 8f21f80a504c7fb834af331715a0661707d25537
workflow graph transform.cwl

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

Path: workflows/fastq_readgroup_stats/transform.cwl

Branch/Commit ID: 3cb464a3a5c39cc060cd23d9c60918bc9ffb169b
workflow graph chipseq-header.cwl

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

Path: metadata/chipseq-header.cwl

Branch/Commit ID: 0fef82b492e03b3588c5e487bd75919d0e936fde
workflow graph kb-tss-preprocess-all.cwl#align-texts-wf.cwl

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/kb-tss-preprocess-all.cwl

Branch/Commit ID: f946a40f63ed03692db7bc5c5bee796eb9432cdb

Packed ID: align-texts-wf.cwl
workflow graph 1st-workflow.cwl

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

Path: v1.0/examples/1st-workflow.cwl

Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e