Explore Workflows

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

Graph Name Retrieved From View
workflow graph Run tRNAScan

https://github.com/ncbi/pgap.git

Path: bacterial_trna/wf_trnascan.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph SV filtering workflow

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

Path: definitions/subworkflows/filter_sv_vcf.cwl

Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9
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