Explore Workflows

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: master

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

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

Path: qa_check_subwf.cwl

Branch/Commit ID: 1.0.0

Runs RNA-Seq BioWardrobe basic analysis with single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-se.cwl

Branch/Commit ID: master

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_seqval_wf_paired_fq.cwl

Branch/Commit ID: 0.2.0

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/ocrevaluation-performance-wf-pack.cwl

Branch/Commit ID: master

Packed ID: main

This workflow aligns the fastq files using STAR for paired-end samples to be used in circRNA pipeline

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Alignments/star-alignment-circRNA.cwl

Branch/Commit ID: master

https://github.com/mnneveau/cancer-genomics-workflow.git

Path: pindel/workflow.cwl

Branch/Commit ID: master

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

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

Branch/Commit ID: 8515542

https://github.com/mnneveau/cancer-genomics-workflow.git

Path: qc/workflow_wgs.cwl

Branch/Commit ID: master

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

Path: subworkflows/exomeseq-gatk4-03-organizedirectories.cwl

Branch/Commit ID: develop