Explore Workflows

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

Graph	Name	Retrieved From	View
	lobSTR-workflow.cwl	https://github.com/common-workflow-language/cwlviewer.git Path: src/test/resources/cwl/lobstr-v1/lobSTR-workflow.cwl Branch/Commit ID: 2e0114d3a1d9c0434e0334a21fa02da682d13d46
	Merge, annotate, and generate a TSV for SVs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022
	Filter differentially expressed genes from DESeq for Tag Density Profile Analyses Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.	https://github.com/datirium/workflows.git Path: workflows/filter-deseq-for-heatmap.cwl Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5
	beast-2step-workflow.cwl	https://github.com/GusEllerm/CWL_workflows.git Path: workflows/BEAST_examples/beast-2step-workflow.cwl Branch/Commit ID: 2c9b239c9a6278303c68357763bc9481a2ac1a3f
	Alignment without BQSR	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sequence_to_bqsr_nonhuman.cwl Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022
	SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.	https://github.com/datirium/workflows.git Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5
	Vcf concordance evaluation workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/vcf_eval_concordance.cwl Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
	extract_gencoll_ids	https://github.com/ncbi/pgap.git Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: f1eb0f4eaaf1661044f28d859f7e8d4302525ead
	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: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5
	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: 2979b565f88ceebca934611adbf3fb8cefd65a19