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Graph Name Retrieved From View
workflow graph trim-rnaseq-pe-dutp.cwl

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

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

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: cf107bc24a37883ef01b959fd89c19456aaecc02
workflow graph qc_workflow.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: bccb338be356db83ad178be2aa9634ae86cb5211
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: 5c0d21fe4f180730d4f6dd301e785bd6b00d5907
workflow graph compile1.cwl#main

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

Path: workflows//compile/compile1.cwl

Branch/Commit ID: master

Packed ID: main
workflow graph xenbase-sra-to-fastq-pe.cwl

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

Path: subworkflows/xenbase-sra-to-fastq-pe.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b
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: subworkflows/heatmap-prepare.cwl

Branch/Commit ID: 3e2ad9c049ea96584c365559c687205e3b642146
workflow graph limit_detection.cwl

https://github.com/andersgs/cwl_flows.git

Path: limit_detection/limit_detection.cwl

Branch/Commit ID: master
workflow graph seqtk_sample_PE.cwl

https://github.com/andersgs/cwl_flows.git

Path: limit_detection/seqtk_sample_PE.cwl

Branch/Commit ID: master
workflow graph zip_and_index_vcf.cwl

This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output.

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: zip_and_index_vcf.cwl

Branch/Commit ID: 40bf56daf9edab82e0f964dbd6961ca1111cd35f
workflow graph workflow_localfiles.cwl

https://github.com/jarnolaitinen/RD_pipeline.git

Path: workflow_localfiles.cwl

Branch/Commit ID: c87304bce01c87346bf1b83558e18120ee834d28