Explore Workflows

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

Graph Name Retrieved From View
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: 687116aeadebda243e8616e0eda2df4c9466c0bf
workflow graph scatter-wf1_v1_2.cwl

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

Path: testdata/scatter-wf1_v1_2.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1
workflow graph workflow1_11.cwl#QualityFilterOuter.cwl

https://github.com/GeorgeAlehandro/cwl_1_11.git

Path: workflow1_11.cwl

Branch/Commit ID: 46d4472af75afacfb13ed92d149a4decd015cf43

Packed ID: QualityFilterOuter.cwl
workflow graph pipeline.cwl

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: 2e31b8ddd4d509c7bbcb983ad41e401687623ddb
workflow graph scatter-wf1_v1_1.cwl

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

Path: testdata/scatter-wf1_v1_1.cwl

Branch/Commit ID: e78db9870cb744fe36674f43b3223c688e9989e1
workflow graph decentralizedFL.cwl

https://github.com/CWL-FLOps/DecentralizedFL-CWL.git

Path: CWL_Workflow/decentralizedFL.cwl

Branch/Commit ID: 08e2a93bb1ec71bd02ff2c3470e39d703715fa59
workflow graph revsort-single-no-docker.cwl

Reverse the lines in a document, then sort those lines.

 https://github.com/Duke-GCB/calrissian.git

Path: input-data/revsort-single-no-docker.cwl

Branch/Commit ID: 4fd8e7dbcff5492cb32e4fb15263a51fa4490cf1
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: c7c674b873b9925b28ffbd602974eec4bfe78cf9
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: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Seed Search Compartments

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

Path: protein_alignment/wf_seed.cwl

Branch/Commit ID: c7c674b873b9925b28ffbd602974eec4bfe78cf9