Explore Workflows

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

Graph Name Retrieved From View
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph concat.cwl

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

Path: cwl/concat.cwl

Branch/Commit ID: 45604eaeea15030c7302941c761464ce392abf74
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Read quality control, trimming and contamination filter.

Workflow for (paired) read quality control, trimming and contamination filtering. Will output a merged set of read pairs, when multiple datasets are used. Steps: - FastQC (read quality control) - fastp (read quality trimming) - Kraken2 taxonomic classification of reads - bbduk used for phix and/or rrna filtering - bbmap for (contamination) filtering

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_illumina_quality.cwl

Branch/Commit ID: cd0c19d51068c5407cd70b718a561d4662819d87
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: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph alignment for nonhuman with qc

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

Path: definitions/pipelines/alignment_wgs_nonhuman.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

https://github.com/datirium/workflows.git

Path: workflows/intervene.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b
workflow graph bwa_mem

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

Path: structuralvariants/cwl/subworkflows/bwa_mem.cwl

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c