Explore Workflows

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Graph	Name	Retrieved From	View
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 04d21c33a5f2950e86db285fa0a32a6659198d8a
	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: 04d21c33a5f2950e86db285fa0a32a6659198d8a
	exome alignment with qc	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_exome.cwl Branch/Commit ID: 87faba2fff8007ecc95160729b1c7cd0376e46f2
	Detect Variants workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/detect_variants.cwl Branch/Commit ID: 87faba2fff8007ecc95160729b1c7cd0376e46f2
	phase VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/phase_vcf.cwl Branch/Commit ID: 9161ef43f7bf0e22b365fde9ec92edcb8601798e
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 9161ef43f7bf0e22b365fde9ec92edcb8601798e
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: 9e5f228bc1a3d0dfe950b5d41d7e4319e834a6d4
	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: 8bf36bfad5624fbc8fc315e82783a44e9e5e4470
	Bisulfite QC tools	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bisulfite_qc.cwl Branch/Commit ID: 9161ef43f7bf0e22b365fde9ec92edcb8601798e
	bacterial_kmer	https://github.com/ncbi/pgap.git Path: bacterial_kmer/wf_bacterial_kmer.cwl Branch/Commit ID: 4f4448f71645275db5b84eb551990dfe3bf37cbb