Explore Workflows

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-snv-indel-annotation.git

Path: pcawg_annotate_wf.cwl

Branch/Commit ID: 1.0.0

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git

Path: preprocess_vcf.cwl

Branch/Commit ID: develop

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

Path: cl-tools/workflow/basic.cwl

Branch/Commit ID: master

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/sorter.cwl

Branch/Commit ID: master

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

Path: workflows/emg-pipeline-v3-paired.cwl

Branch/Commit ID: master

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

https://github.com/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: master

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: master

https://github.com/jeremiahsavage/toy-cwl.git

Path: touch_ls_wf.cwl

Branch/Commit ID: master

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

Path: workflows/sanbi_cwltutorial/revcomp/revcomp_with_rename.cwl

Branch/Commit ID: master

Example CWL workflow that uses some advanced features

https://github.com/mskcc/pluto-cwl.git

Path: cwl/example_workflow.cwl

Branch/Commit ID: master