Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

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

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: a0b22644ca178b640fb74849d23b7c631022f0b5
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph filter_alignment_artifacts.cwl

GATK4.1.2 Alignment artifacts filtration workflow

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

Path: subworkflows/filter_alignment_artifacts.cwl

Branch/Commit ID: 58b62b1bf329b3fbffbd5d9080709999bebc1763
workflow graph standard_bam_to_collapsed_qc.cwl

This is a workflow to go from standard bams to collapsed bams and QC results.

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

Path: workflows/subworkflows/standard_bam_to_collapsed_qc.cwl

Branch/Commit ID: b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf
workflow graph mutect2_calling.cwl

GATK4.1.2 Mutect2 workflow

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

Path: subworkflows/mutect2_calling.cwl

Branch/Commit ID: 58b62b1bf329b3fbffbd5d9080709999bebc1763
workflow graph calculate_contamination_workflow.cwl

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: 58b62b1bf329b3fbffbd5d9080709999bebc1763
workflow graph allele-rnaseq-pe.cwl

Allele specific RNA-Seq paired-end workflow

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

Path: workflows/allele-rnaseq-pe.cwl

Branch/Commit ID: 62323c137c0ce9b3f843df0dfbda28dafa7c90cf