Explore Workflows

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

Graph Name Retrieved From View
workflow graph workflow.cwl

https://github.com/screx/cwl-tutorial.git

Path: bioinformatics/tools/workflow.cwl

Branch/Commit ID: master
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 STAR-Alignment-PE

This workflow aligns the fastq files using STAR for no spliced genomes

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

Path: workflows/Alignments/star-alignment-nosplice.cwl

Branch/Commit ID: b5a440939ac6022ee81aeeb0dd7daf3983228a61
workflow graph conflict.cwl#main

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

Path: tests/wf/conflict.cwl

Branch/Commit ID: main

Packed ID: main
workflow graph ValidateTriggerPerformance

Compare trigger performance between simulations and data.

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

Path: workflows/ValidateTriggerPerformance.cwl

Branch/Commit ID: main
workflow graph wf_demultiplex_se.cwl

This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)

https://github.com/YeoLab/eclip.git

Path: cwl/wf_demultiplex_se.cwl

Branch/Commit ID: master
workflow graph batch-preprocess-ont.cwl

https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git

Path: PreProcessing/batch-preprocess-ont.cwl

Branch/Commit ID: master
workflow graph rna-seq-pipeline.cwl

https://github.com/sbg/sbg_dockstore_tools.git

Path: gtex-rnaseq-pipeline/rna-seq-pipeline.cwl

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

RNA-seq 02 trimming - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

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

Branch/Commit ID: master
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: main