Explore Workflows

Restore the contig names using the map file

https://github.com/EBI-Metagenomics/emg-viral-pipeline.git

Path: cwl/src/Tools/FastaRename/fasta_restore_swf.cwl

Branch/Commit ID: aad5474411ea31449b3e8a26eeed8920dd07fa17

https://github.com/NCI-GDC/gdc-rnaseq-cwl.git

Path: rnaseq-star-align/subworkflows/rnaseq_processing/rnaseq_metrics_workflow.cwl

Branch/Commit ID: 88fb720c62a3c2b00ca475d412fba088c4a08f92

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_apollo2_data_processing/processing/workflow.cwl

Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f

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: 4a93f8fcd34a25427b4ade8afe1772a3287fcf1e

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

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

Branch/Commit ID: 5e8217435bcdd597b2ad236f3e847d13d4c21824

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: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf

https://github.com/biosciencedbc/jga-analysis.git

Path: per-sample/Workflows/bams2cram.cwl

Branch/Commit ID: main

Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files

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

Path: cwl/igv-report_maf_workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933

https://github.com/EBI-Metagenomics/workflow-is-cwl.git

Path: workflows/TranscriptomeAssembly-wf.single-end.cwl

Branch/Commit ID: 72f702591368397f56d455128f60916902104dd2

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

Path: tests/io-any-wf-1.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de