Explore Workflows

Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups

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

Path: workflows/subworkflows/find_hotspots_in_normals.cwl

Branch/Commit ID: master

GATK4.1.2 Calculate tumor-normal contamination workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/calculate_contamination_workflow.cwl

Branch/Commit ID: master

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

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 0fed1c9

https://github.com/hubmapconsortium/sprm.git

Path: pipeline.cwl

Branch/Commit ID: d2d5127

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: master

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/AddBamStatsSomatic_v0_1_0.cwl

Branch/Commit ID: master

https://github.com/mr-c/4dn-dcic-pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-pairs-nore-nonorm.cwl

Branch/Commit ID: dev2

https://github.com/YeoLab/eclip.git

Path: cwl/wf_get_peaks_nostats_se.cwl

Branch/Commit ID: master

https://github.com/hubmapconsortium/ome-tiff-pyramid.git

Path: pipeline.cwl

Branch/Commit ID: b1b40c4

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_alignment_wf.cwl

Branch/Commit ID: master