Explore Workflows

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

Graph Name Retrieved From View
workflow graph pcawg_minibam_wf.cwl

This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `

https://github.com/ICGC-TCGA-PanCancer/pcawg-minibam.git

Path: pcawg_minibam_wf.cwl

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

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

Path: pipeline.cwl

Branch/Commit ID: baee233
workflow graph validate_interleaved_fq.cwl

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/validate_interleaved_fq.cwl

Branch/Commit ID: 0.4.0
workflow graph 04-quantification-pe-revstranded.cwl

RNA-seq 04 quantification

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

Path: v1.0/RNA-seq_pipeline/04-quantification-pe-revstranded.cwl

Branch/Commit ID: master
workflow graph cnv.cwl

Copynumber variation workflow, runs ADTEx and Varscan

 https://github.com/BD2KGenomics/dockstore_workflow_cnv.git

Path: cnv.cwl

Branch/Commit ID: 1.0.1
workflow graph snapanalysis_setup_and_analyze.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/snapanalysis_setup_and_analyze.cwl

Branch/Commit ID: 302f1f3
workflow graph star_samtools_stringtie-prepDE-DESeq2.htseq-dexseq.cwl

https://github.com/rawgene/cwl.git

Path: workflows/star_samtools_stringtie-prepDE-DESeq2.htseq-dexseq.cwl

Branch/Commit ID: master
workflow graph Water body detection based on NDWI and the otsu threshold

Water bodies detection based on NDWI and otsu threshold applied to Sentinel-2 or Landsat-9 staged acquisitions

 https://github.com/eoap/mastering-app-package.git

Path: cwl-workflow/app-water-body.cwl

Branch/Commit ID: main

Packed ID: water-bodies
workflow graph Metagenomic Binning from Assembly

Workflow for Metagenomics from raw reads to annotated bins.<br> Summary - MetaBAT2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification) - BUSCO (bin completeness) **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br>

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_binning.cwl

Branch/Commit ID: master
workflow graph magicblast-alignment-pe

This workflow aligns the fastq files using magicblast for paired-end samples

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

Path: workflows/Alignments/magicblast-alignment.cwl

Branch/Commit ID: master