Explore Workflows

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: 34d0ad68878b24aa1ffd8d8b8f7b8b2f5fd82787

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: ca75d68eb74c93b35b404ec7908dc5b260e16466

ATAC-seq pipeline - reads: SE

https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/pipeline-se.cwl

Branch/Commit ID: 3a4314c66c1eb090e656af5a0d388cec87d65318

rna / protein - qc, annotation, index, abundance

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

Path: CWL/Workflows/assembled.workflow.cwl

Branch/Commit ID: 49e29dfc5b1f7a7630831a1052f9136caa29dbf7

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

Path: metadata/indices-header.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c

BAM filtering

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

Path: structuralvariants/cwl/subworkflows/bam_filtering.cwl

Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c

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

Path: tests/env-wf2.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

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

Path: definitions/pipelines/detect_variants_mouse.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf2.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389