Explore Workflows

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-core-analysis-v4.cwl

Branch/Commit ID: ecf044f3a5a7589cb2238487a19f22863c2bcdb1

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/datirium/workflows.git

Path: tools/heatmap-prepare.cwl

Branch/Commit ID: b1a5dabeeeb9079b30b2871edd9c9034a1e00c1c

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: bcc6adaf15035f5ce6fc851e27b1173b0fd20c1c

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/collate_unique_SSU_headers.cwl

Branch/Commit ID: 71d9c83761ea301a895dd669902979ef5a4b279b

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/wgs-processing-wf.cwl

Branch/Commit ID: ef89d0aabd706c59168537f69742e570373fdd84

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v4-assembly-metaSPAdes.cwl

Branch/Commit ID: ecf044f3a5a7589cb2238487a19f22863c2bcdb1

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: 812b0ff40dda18ab7a9a872ff13a577be8531ba6

This workflow creates tagAlign file

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/create-tagAlign.cwl

Branch/Commit ID: 8902d8d5dc85ee568decc2de51f7694164f32b00

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: d3b8e458b7f9e52a12c0008aca645de9230e8bc9

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

Path: tests/record-in-secondaryFiles-wf.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912