Explore Workflows

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

Graph Name Retrieved From View
workflow graph somatic_exome: exome alignment and somatic variant detection

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f
workflow graph exome alignment with qc

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

Path: definitions/pipelines/exome_alignment.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph transcriptome_cleanup

This workflow detect and remove vector, duplicate and contamination from a transcriptome fasta file

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

Path: workflows/Annotation/transcriptome-cleanup.cwl

Branch/Commit ID: e6efd0c93582ad6435ed10020544ef8982a25a8e
workflow graph count-lines1-wf-noET.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines1-wf-noET.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5
workflow graph wffail.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/wffail.cwl

Branch/Commit ID: 31aa094dce60cbb176229d6b918bfd5ae09c0390
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 3ee63d8757c341ca98b3b46ec4782862ad19b710
workflow graph cond-single-source-wf-005.1.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/cond-single-source-wf-005.1.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507
workflow graph env-wf3.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/env-wf3.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4