Explore Workflows

https://github.com/msk-access/qc_generation.git

Path: access_qc__packed.cwl

Branch/Commit ID: develop

Packed ID: bam_qc_stats.cwl

This workflow convert fastq to multiple fasta files

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

Path: workflows/File-formats/fastq-to-splitted-fasta.cwl

Branch/Commit ID: master

This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2

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

Path: workflows/standard_pipeline.cwl

Branch/Commit ID: master

Workflow without outputs.

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

Path: tests/no-outputs-wf.cwl

Branch/Commit ID: master

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

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

Path: preprocessor_for_oxog.cwl

Branch/Commit ID: 1.0.0

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

Path: v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: master

VDJ_SplitValidReads splits fasta files to be multi-processed in the VDJ step.

https://github.com/longbow0/cwl.git

Path: v1.9-beta/rhapsody_targeted_1.9-beta.cwl

Branch/Commit ID: master

Packed ID: VDJ_SplitValidReads.cwl

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: e4d42b85d24cd5088e14cc31d67c2dee0c6fc40a

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

Path: pipeline.cwl

Branch/Commit ID: b9c8e26

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/ocrevaluation-performance-test-files-wf-pack.cwl

Branch/Commit ID: master

Packed ID: main