Explore Workflows

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

Graph	Name	Retrieved From	View
	snapanalysis_setup_and_analyze.cwl	https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git Path: steps/snapanalysis_setup_and_analyze.cwl Branch/Commit ID: bb023f95ca3330128bfef41cc719ffcb2ee6a190
	cnv_exomedepth CNV ExomeDepth calling	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: 637e294ff72687314faacef2c30cb46874611e50
	Running cellranger count and lineage inference	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/single_cell_rnaseq.cwl Branch/Commit ID: e56f1024306aeb427d8aae2fff715ed2e8b8f86f
	nanopore_bcr_abl_umi_analysis.cwl	https://github.com/teoloup/nanopore_fusion.git Path: nanopore_bcr_abl_umi_analysis.cwl Branch/Commit ID: 9bbba11454dd9f3a977797149026088eddd5c41f
	scatter-valuefrom-wf5.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/scatter-valuefrom-wf5.cwl Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e
	bam to trimmed fastqs and biscuit alignments	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
	bact_get_kmer_reference	https://github.com/ncbi/pgap.git Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 909f26beaf96c2cdfe208f87ecd1e9c3de20b81c
	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: a8909e86f5bcb048d136f9a7d70b4b6f8f4e485f
	count-lines10-wf.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/count-lines10-wf.cwl Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e
	Salmon quantification, FASTQ -> H5AD count matrix	https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git Path: salmon-rnaseq/steps/salmon-quantification.cwl Branch/Commit ID: c338cd390c994eb3601cc7749878add1056953ba