Explore Workflows

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

Graph	Name	Retrieved From	View
	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: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
	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: 935a78f1aff757f977de4e3672aefead3b23606b
	workflow.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_dispatch/2other_species/workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
	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: 1750cd5cc653f058f521b6195e3bec1e7df1a086
	WGS QC workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_wgs.cwl Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9
	Interval overlapping alignments counts Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.	https://github.com/datirium/workflows.git Path: workflows/bedtools-multicov.cwl Branch/Commit ID: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86
	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: 6f9f8a2057c6a9f221a44559f671e87a75c70075
	Cell Ranger Count Gene Expression Cell Ranger Count Gene Expression =================================	https://github.com/datirium/workflows.git Path: workflows/single-cell-preprocess-cellranger.cwl Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b
	WGS QC workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/qc_wgs.cwl Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075
	Immunotherapy Workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/immuno.cwl Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c