Explore Workflows

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

Graph	Name	Retrieved From	View
	phase VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/phase_vcf.cwl Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
	baysorStaged.cwl	https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git Path: steps/baysorStaged.cwl Branch/Commit ID: e7f46046a7338b6a2bb914e263278ea9c0207326
	sequence (bam or fastqs) to trimmed fastqs and HISAT alignments	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sequence_to_trimmed_fastq_and_hisat_alignments.cwl Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
	bact_get_kmer_reference	https://github.com/ncbi/pgap.git Path: task_types/tt_bact_get_kmer_reference.cwl Branch/Commit ID: 2c7879b47890b9300ab9b5ebd35e17372e077757
	SV filtering workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/filter_sv_vcf.cwl Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
	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: 4f48ee6f8665a34cdf96e89c012ee807f80c7a3d
	sorter.cwl	https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git Path: steps/sorter.cwl Branch/Commit ID: e7f46046a7338b6a2bb914e263278ea9c0207326
	adapter for sequence_align_and_tag Some workflow engines won't stage files in our nested structure, so parse it out here	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
	SSU-from-tablehits.cwl	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 2104dc36c775de93de3fef77e7f82a19da76b6e3
	segmentation.cwl	https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git Path: steps/segmentation.cwl Branch/Commit ID: e7f46046a7338b6a2bb914e263278ea9c0207326