Explore Workflows

BAM filtering

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: 1.0.7

https://github.com/epigenomics-screw/screw.git

Path: cwl/preprocess.cwl

Branch/Commit ID: scatter

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

Path: workflows/dnaseq/metrics.cwl

Branch/Commit ID: 1.0

Whole Exome Sequence analysis using GATK4 - v2.2.0

https://github.com/bespin-workflows/exomeseq-gatk4.git

Path: exomeseq-gatk4.cwl

Branch/Commit ID: develop

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-blast-ebeye-pdbe.cwl

Branch/Commit ID: master

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

Path: tools/LSU-from-tablehits.cwl

Branch/Commit ID: 71d9c83

This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `

https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: oxog_varbam_annotate_wf.cwl

Branch/Commit ID: master

https://github.com/reanahub/reana-demo-helloworld.git

Path: workflow/cwl/helloworld-htcondorcern.cwl

Branch/Commit ID: master

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: main

https://github.com/alahiff/fastwf.git

Path: mast.cwl

Branch/Commit ID: master