Explore Workflows

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883

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: b4b7b2e7e508be5eac639f9e323d141daf714c0d

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

Path: cwltool/schemas/v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: 203797516329f7fb8aa5e763e6f9b331c63c3060

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

Path: tests/io-any-wf-1.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: ae401a813472ca453a99ad067a5e6fc3bd71112b

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

Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

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

Path: workflows/xenbase-fastq-bowtie-bigwig-se-pe.cwl

Branch/Commit ID: 4b8bb1a1ec39056253ca8eee976078e51f4a954e

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

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4

Packed ID: main

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: e0b3c76e38630fb6234414b5adebfb6a4fb23117