Explore Workflows

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

Graph Name Retrieved From View
workflow graph ChIP-seq peak caller workflow MACS2 based

This workflow execute peak caller and QC for ChIP-seq using MACS2

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

Path: workflows/ChIP-Seq/peak-calling-MACS2.cwl

Branch/Commit ID: master
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

https://github.com/mr-c/datirium-workflows.git

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: license_test
workflow graph count-lines1-wf.cwl

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

Path: tests/count-lines1-wf.cwl

Branch/Commit 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: CWLProvTesting
workflow graph env-wf3.cwl

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

Path: tests/env-wf3.cwl

Branch/Commit ID: master
workflow graph rRNA_selection.cwl

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 9c57dba
workflow graph scRNA-seq pipeline using Salmon and Alevin

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: pipeline.cwl

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

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

Path: unaligned_bam_to_bqsr/align.cwl

Branch/Commit ID: toil_compatibility
workflow graph Production Configuration

This workflow prepares the configuration of the subsequent production steps.

https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git

Path: workflows/wms/uc-wms-XXX.cwl

Branch/Commit ID: main
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: master