Explore Workflows

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

Graph Name Retrieved From View
workflow graph tmb.cwl

Workflow for calculating TMB tumor mutational burden on a single sample

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

Path: cwl/tmb.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph maf2vcf_gz_workflow.cwl

Workflow to convert a maf file into a vcf.gz with .tbi index

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

Path: cwl/maf2vcf_gz_workflow.cwl

Branch/Commit ID: e19ef998e906eb915cf4351a3599abd9bff57205
workflow graph msi_workflow.cwl

Workflow to run the MSI analysis on a batch of samples and merge the results back into a single data clinical file

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

Path: cwl/msi_workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph consensus_bed.cwl

Workflow to merge a large number of maf files into a single consensus bed file

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

Path: cwl/consensus_bed.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph concat.cwl

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

Path: cwl/concat.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using GATK4. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.

https://github.com/leipzig/2020-covid-19-bh.git

Path: Ambarish_Kumar_SOP/CWL/Ambarish_Kumar_SOP-GATK-SAR-CoV-2.cwl

Branch/Commit ID: 63315ece5c005f6dc8bd8b0401aaf7ae8d35e91a
workflow graph workflow.cwl

https://github.com/morgantaschuk/one-workflow-many-ways.git

Path: cwl/workflow.cwl

Branch/Commit ID: 978fb8734948c36942b26b6c0a06581b0f2b1ff6
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fastq.workflow.cwl

Branch/Commit ID: 091374dc59a23966338638a668ae397d4ee20b2f
workflow graph analysis for assembled sequences

rna / protein - qc, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/assembled.workflow.cwl

Branch/Commit ID: 091374dc59a23966338638a668ae397d4ee20b2f
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fasta.workflow.cwl

Branch/Commit ID: 091374dc59a23966338638a668ae397d4ee20b2f