Explore Workflows

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

Graph Name Retrieved From View
workflow graph bqsr-flow.cwl

Run BQSR pre+post+plot flow

 https://github.com/sentieon/sentieon-cwl.git

Path: stage/bqsr-flow.cwl

Branch/Commit ID: d20382adfe7285cb517a25d95d2bcb7586546e23
workflow graph Gathered Downsample and HaplotypeCaller

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

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph genomics-workspace-genome.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_genomicsWorkspace/genomics-workspace-genome.cwl

Branch/Commit ID: 556884e8e205295e561b1d9140d836cdd6c1d8c9
workflow graph kfdrc_alignment_wf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_alignment_wf.cwl

Branch/Commit ID: d4e818c8b9bf56c83694639aa542bb5c1a174f7d
workflow graph no-inputs-wf.cwl

Workflow without inputs.

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

Path: tests/no-inputs-wf.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph EMG assembly for paired end Illumina

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-assembly.cwl

Branch/Commit ID: 56dafa4dab5892c5afa35713563dddc78ec5a00d
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
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/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: cf84038de256c7ca98657ad81734d1aca1dad8c1