Explore Workflows

GATK4.2.4.1 Mutect2 workflow

https://github.com/NCI-GDC/gatk4_mutect2_cwl.git

Path: subworkflows/gatk4.2.4.1_mutect2_workflow.cwl

Branch/Commit ID: master

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

Path: packed/exomeseq.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: exomeseq-01-preprocessing.cwl

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: master

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

Path: tests/step-valuefrom4-wf.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/search.cwl

Branch/Commit ID: master

Packed ID: main

This workflow is intended to be used to test the QC module, without having to run the long waltz step

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow_wo_waltz.cwl

Branch/Commit ID: master

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

Path: v1.0/v1.0/count-lines11-null-step-wf-noET.cwl

Branch/Commit ID: master

Worfklow combining an SRA fetch from NCBI with a fastq-dump cmd

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

Path: bio-cwl-tools/sratoolkit/prefetch_fastq.cwl

Branch/Commit ID: preprocessing

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/common-workflow-library/bio-cwl-tools.git

Path: bwa/BWA-Mem2-single.cwl

Branch/Commit ID: release