Explore Workflows

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

Graph Name Retrieved From View
workflow graph mosdepth_to_coverage_QC.cwl

https://github.com/YinanWang16/tso500-ctdna-post-processing.git

Path: cwl/workflows/mosdepth_to_coverage_QC.cwl

Branch/Commit ID: 08f855a08ca02b15c8d3540b28bb17b4f85a371a
workflow graph 02-trim-se.cwl

RNA-seq 02 trimming - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: ebd63f705d0fde7290e42c8300d5420c25cfbfe3
workflow graph 04-quantification-se-revstranded.cwl

RNA-seq 04 quantification

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/04-quantification-se-revstranded.cwl

Branch/Commit ID: ebd63f705d0fde7290e42c8300d5420c25cfbfe3
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: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
workflow graph sec-wf-out.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: 596aab620489cd2611f4bc1d9a4fc914ddf34514
workflow graph CLE gold vcf evaluation workflow

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

Path: definitions/subworkflows/vcf_eval_cle_gold.cwl

Branch/Commit ID: 10870aefd20469e728969269ff3c54b3b8339a18
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: be5ae41801b19ebc69a2889d8fdb39e8e2359611
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: 3a822294da63b4e19446a285e2fef075e23cf3d0
workflow graph alignment-pair.cwl

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

Path: modules/pair/alignment-pair.cwl

Branch/Commit ID: 46eddf1e191352cad5e95dd3c24eeae3738da485
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 10870aefd20469e728969269ff3c54b3b8339a18