Explore Workflows

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

Graph	Name	Retrieved From	View
	directory.cwl Inspect provided directory and return filenames. Generate a new directory and return it (including content).	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/directory.cwl Branch/Commit ID: 8ef515037de411abd2f84b569ad4d4a4f7a2c7a0
	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/datirium/workflows.git Path: tools/bam-bedgraph-bigwig.cwl Branch/Commit ID: c5bae2ca862c764911b83d1f15ff6af4e2a0db28
	Exome QC workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
	tt_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 72c3091012f5c2dce38ad9213cda617d2c7a61ac
	kmer_cache_store	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: d87a0786b52809b36201adb7d3d3ab2b8bbbef20
	allele-process-strain.cwl	https://github.com/Barski-lab/workflows.git Path: subworkflows/allele-process-strain.cwl Branch/Commit ID: f2aee86fecd321efc6857b124350f079238ea2ba
	wgs alignment with qc	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/wgs_alignment.cwl Branch/Commit ID: a670f323e77e02d9b77be9a13d73d5276dd3676c
	bact_get_kmer_reference	https://github.com/ncbi/pgap.git Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 8cc9b995bca666c54c673a5eb8d9b8c6f8e84490
	echo-wf-default.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/echo-wf-default.cwl Branch/Commit ID: 7c7615c44b80f8e76e659433f8c7875603ae0b25
	timelimit-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/timelimit-wf.cwl Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4