Explore Workflows

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

Graph	Name	Retrieved From	View
	xenbase-fastq-bowtie-bigwig-se-pe.cwl	https://github.com/datirium/workflows.git Path: subworkflows/xenbase-fastq-bowtie-bigwig-se-pe.cwl Branch/Commit ID: d6ec0dee61ef65a110e10141bde1a79332a64ab0
	pangenome-generate.cwl	https://github.com/arvados/bh20-seq-resource.git Path: workflows/pangenome-generate/pangenome-generate.cwl Branch/Commit ID: fdb1b012fc04ee07f401541e181e28fe442c9454
	workflow.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_dispatch/2other_species/workflow.cwl Branch/Commit ID: 0ecf492419ddaa015f14a163381948c53b3deea6
	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/icgc-tcga-pancancer/pcawg-oxog-filter.git Path: zip_and_index_vcf.cwl Branch/Commit ID: 123a3151d35f98e442e703d903dc3e1d72f3c4b0
	oxog_sub_wf.cwl This is a subworkflow - this is not meant to be run as a stand-alone workflow!	https://github.com/icgc-tcga-pancancer/pcawg-oxog-filter.git Path: oxog_sub_wf.cwl Branch/Commit ID: 123a3151d35f98e442e703d903dc3e1d72f3c4b0
	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/datirium/workflows.git Path: tools/heatmap-prepare.cwl Branch/Commit ID: 799575ce58746813f066a665adeacdda252d8cab
	allele-process-reference.cwl	https://github.com/datirium/workflows.git Path: subworkflows/allele-process-reference.cwl Branch/Commit ID: e627079d8431e4f1f1c7531af1ca2e7dcc684b90
	Transcriptome assembly workflow (paired-end version)	https://github.com/mscheremetjew/workflow-is-cwl.git Path: workflows/TranscriptomeAssembly-wf.paired-end.cwl Branch/Commit ID: e9bbe2917384efc75ba067db23612bc8e22f3f06
	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: 64e85970dbecba89c3380ab285c108d221e76fe6
	indexing_bed	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/cwl/abstract_operations/subworkflows/indexing_bed.cwl Branch/Commit ID: 82e533a98a763a258bd841ed0032c79445478d56