Explore Workflows

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

Graph Name Retrieved From View
workflow graph 02-trim-pe.cwl

RNA-seq 02 trimming - reads: PE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: 71146d85ae7f0c562ec0d454fbbb7085a827356e
workflow graph 02-trim-se.cwl

RNA-seq 02 trimming - reads: SE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: 71146d85ae7f0c562ec0d454fbbb7085a827356e
workflow graph 01-qc-se.cwl

RNA-seq 01 QC - reads: SE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/01-qc-se.cwl

Branch/Commit ID: 71146d85ae7f0c562ec0d454fbbb7085a827356e
workflow graph compile1.cwl#main

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

Path: workflows/compile/compile1.cwl

Branch/Commit ID: 05144d9652daa185b131371251d593f079b8cd8d

Packed ID: main
workflow graph TOPMed_RNA-seq

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows) 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/FarahZKhan/cwl_workflows.git

Path: topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl

Branch/Commit ID: 027e8af41b906173aafdb791351fb29efc044120
workflow graph transform.cwl

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

Path: workflows/bamfastq_align/transform.cwl

Branch/Commit ID: ff015418f870bdfbd82ba675eb549fe8b4584b0c
workflow graph 01-qc-pe.cwl

RNA-seq 01 QC - reads: PE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/01-qc-pe.cwl

Branch/Commit ID: 71146d85ae7f0c562ec0d454fbbb7085a827356e
workflow graph wf-variantcall.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: somatic-giab-mix/somatic-giab-mix-workflow/wf-variantcall.cwl

Branch/Commit ID: afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9
workflow graph Unaligned to aligned BAM

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

Path: unaligned_bam_to_bqsr/align.cwl

Branch/Commit ID: ee1afbcbe01fd17715b54d23e556a23086aeec57
workflow graph main-pisces-ras.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: somatic-lowfreq/pisces-ras-workflow/main-pisces-ras.cwl

Branch/Commit ID: afd674a6d64fb4e115c0b3fe95b7bb1b73ec69a9