Explore Workflows

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

Graph Name Retrieved From View
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 48381989cb983567ed936fde632714933df65350
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: d09a44ebc8d092ffd8370a324c9e84b37a593d38
workflow graph protein annotation

Proteins - predict, filter, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-filter-annotation.workflow.cwl

Branch/Commit ID: 2addcde0f4c1c8547f7f3906c2523cded23e9869
workflow graph heatmap-prepare.cwl

Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.

https://github.com/Barski-lab/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: 144eee15187c1a1145ce1ee0239da69059fd2752
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph Unaligned BAM to BQSR and VCF

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 92bdcd9fa879161834ecdb1c4c9ac7c46e940206
workflow graph rna annotation

RNAs - predict, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/rna-annotation.workflow.cwl

Branch/Commit ID: 2addcde0f4c1c8547f7f3906c2523cded23e9869
workflow graph step-valuefrom3-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/step-valuefrom3-wf.cwl

Branch/Commit ID: a22b7580c6b50e77c0a181ca59d3828dd5c69143
workflow graph main-autofraginfo.cwl

https://github.com/kyusque/abmp_log_dump2pieda.git

Path: main-autofraginfo.cwl

Branch/Commit ID: 36d894eed604a2ba8ccaeaa3449f25b4128d224d
workflow graph qc-basic.workflow.cwl

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/qc-basic.workflow.cwl

Branch/Commit ID: 2addcde0f4c1c8547f7f3906c2523cded23e9869