Explore Workflows

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

Graph	Name	Retrieved From	View
	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: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e
	workflow.cwl	https://github.com/NAL-i5K/Organism_Onboarding.git Path: flow_dispatch/2other_species/workflow.cwl Branch/Commit ID: 3aabbb0f6635bb9354ad52f616ab7cfc61848eb6
	Subworkflow to allow calling different SV callers which require bam files as inputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 06d2440d115b446c299b4ce96e8812d2f8df86ec
	Super-enhancer post ChIP-Seq analysis Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)	https://github.com/datirium/workflows.git Path: workflows/super-enhancer.cwl Branch/Commit ID: 1f03ff02ef829bdb9d582825bcd4ca239e84ca2e
	freebayes.cwl	https://github.com/uc-cdis/genomel_pipelines.git Path: genomel/cwl/workflows/variant_calling/freebayes.cwl Branch/Commit ID: 28bb82ba031041321ff9caa5c299ec1bb15d7471
	umi molecular alignment fastq workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_umi_molecular.cwl Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735
	ROSE: rank ordering of super-enhancers Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)	https://github.com/datirium/workflows.git Path: workflows/super-enhancer.cwl Branch/Commit ID: a0b22644ca178b640fb74849d23b7c631022f0b5
	strelka workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/strelka_and_post_processing.cwl Branch/Commit ID: 06d2440d115b446c299b4ce96e8812d2f8df86ec
	Filter single sample sv vcf from depth callers(cnvkit/cnvnator)	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sv_depth_caller_filter.cwl Branch/Commit ID: 742dbafb5fb103d8578f48a0576c14dd8dae3b2a
	bacterial_kmer	https://github.com/ncbi/pgap.git Path: bacterial_kmer/wf_bacterial_kmer.cwl Branch/Commit ID: 3897218b16b30a933beecd60a98a300d677207d8