Explore Workflows

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Graph	Name	Retrieved From	View
	gathered exome alignment and somatic variant detection for cle purpose	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome_cle_gathered.cwl Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
	default-dir5.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/default-dir5.cwl Branch/Commit ID: 8ef515037de411abd2f84b569ad4d4a4f7a2c7a0
	Filter Protein Seeds; Find ProSplign Alignments	https://github.com/ncbi/pgap.git Path: protein_alignment/wf_compart_filter_prosplign.cwl Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
	Gathered Downsample and HaplotypeCaller	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/gathered_downsample_and_recall.cwl Branch/Commit ID: 87faba2fff8007ecc95160729b1c7cd0376e46f2
	Tag enrichment heatmap and density profile around regions of interest Generates tag density heatmap and histogram for the centered list of features in a headerless regions file. - If provided regions file is a gene list with the following columns `chrom start end name score strand` set `Gene TSS` as a re-centering criteria. - If provided regions file is a peak list with the following columns `chrom start end name` set `Peak Center` as a re-centering criteria. `score` column is always ignored.	https://github.com/datirium/workflows.git Path: workflows/heatmap.cwl Branch/Commit ID: 46d3d403ddb240d5a8f4f31ab992b6d6a2686745
	umi per-lane alignment subworkflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/umi_alignment.cwl Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562
	heatmap-prepare.cwl Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.	https://github.com/datirium/workflows.git Path: tools/heatmap-prepare.cwl Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964
	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: 7eef0294395d83ff0765fce61726a59d71126422
	env-wf3.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/env-wf3.cwl Branch/Commit ID: e62f99dd79d6cb9c157cceb458f74200da84f6e9
	kmer_ref_compare_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c