Explore Workflows

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

Graph Name Retrieved From View
workflow graph EMG assembly for paired end Illumina

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

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

Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
workflow graph count-lines14-wf.cwl

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

Path: tests/count-lines14-wf.cwl

Branch/Commit ID: 368b562a1449e8cd39ae8b7f05926b2bfb9b22df
workflow graph preprocess-ont.cwl

https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git

Path: PreProcessing/preprocess-ont.cwl

Branch/Commit ID: 3114ddd28bbee5505a9819b1a84f4896fd0b0992
workflow graph dna.cwl#main

https://bitbucket.org/markrobinson96/workflows.git

Path: workflows/make-to-cwl/dna.cwl

Branch/Commit ID: master

Packed ID: main
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