Explore Workflows

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

Graph	Name	Retrieved From	View
	secret_wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/secret_wf.cwl Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0
	Whole genome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_wgs.cwl Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
	tt_fscr_calls_pass1	https://github.com/ncbi/pgap.git Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: 42df0c0f9a4e5697abadd9cb52440691fafc8f5d
	count-lines13-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl Branch/Commit ID: 7c7615c44b80f8e76e659433f8c7875603ae0b25
	exome alignment with qc, no bqsr, no verify_bam_id	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/exome_alignment_mouse.cwl Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b
	gathered exome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/gathered_somatic_exome.cwl Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
	heatmap.cwl Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension	https://github.com/Barski-lab/workflows.git Path: workflows/heatmap.cwl Branch/Commit ID: 64e85970dbecba89c3380ab285c108d221e76fe6
	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: 5b1d3af2b36d64c15095e62ed0ba7543369f216c
	count-lines10-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl Branch/Commit ID: 4635090ef98247b1902b3c7a25c007d9db1cb883
	scatter-valuefrom-wf4.cwl#main	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/scatter-valuefrom-wf4.cwl Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4 Packed ID: main