Explore Workflows

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

Graph Name Retrieved From View
workflow graph cnv_manta

CNV Manta calling

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

Path: structuralvariants/cwl/subworkflows/cnv_manta.cwl

Branch/Commit ID: 5230874e81911b6591cf859fe794f71f4eb8bb97
workflow graph FASTQ Vector Removal

This workflow clean up vectros from fastq files

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

Path: workflows/File-formats/remove-fastq-reads-from-blast.cwl

Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419
workflow graph samtools_mpileup_subpipeline.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/samtools_mpileup_subpipeline.cwl

Branch/Commit ID: b4550175be9d485d509c61d87fddf88a8bdb70c1
workflow graph VIRTUS.PE.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/VIRTUS.PE.cwl

Branch/Commit ID: 16dbe9d99137cbfee834fc22b79190f812543f7e
workflow graph split_bam_subpipeline.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/split_bam_subpipeline.cwl

Branch/Commit ID: b4550175be9d485d509c61d87fddf88a8bdb70c1
workflow graph Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass2.cwl

Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: 25eab0390f6866ce491b44c89d9e0435d228ab6f
workflow graph bam-bedgraph-bigwig.cwl

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: e45ab1b9ac5c9b99fdf7b3b1be396dc42c2c9620
workflow graph wf_get_peaks_nostats_se.cwl

https://github.com/YeoLab/eclip.git

Path: cwl/wf_get_peaks_nostats_se.cwl

Branch/Commit ID: 49a9bcda10de8f55fab2481f424eb9cdf2e5b256
workflow graph strelkaSomaticVariantCaller_v0_1_1.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl

Branch/Commit ID: b4550175be9d485d509c61d87fddf88a8bdb70c1