Explore Workflows

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

Graph Name Retrieved From View
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 3ee63d8757c341ca98b3b46ec4782862ad19b710
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