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Graph	Name	Retrieved From	View
	Generate ATDP heatmap using Homer Generate ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension	https://github.com/datirium/workflows.git Path: workflows/heatmap.cwl Branch/Commit ID: dda9e6e06a656b7b3fa7504156474b962fe3953c
	Subworkflow to allow calling cnvkit with cram instead of bam files	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cram_to_cnvkit.cwl Branch/Commit ID: 5cb188131f786ed33156e2f0e3dd63ab9c04245d
	Deprecated. RNA-Seq pipeline single-read The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) RNA-Seq basic analysis for a single-read experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file	https://github.com/datirium/workflows.git Path: workflows/rnaseq-se.cwl Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
	umi duplex alignment fastq workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_umi_duplex.cwl Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
	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: 76a35e7d885790f30559beb31f3b58770e343afd
	record-in-secondaryFiles-missing-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/record-in-secondaryFiles-missing-wf.cwl Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
	SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.	https://github.com/datirium/workflows.git Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 34d0ad68878b24aa1ffd8d8b8f7b8b2f5fd82787
	RNA-seq (VCF) alelle specific pipeline for single-read data Allele specific RNA-Seq (using vcf) single-read workflow	https://github.com/datirium/workflows.git Path: workflows/allele-vcf-rnaseq-se.cwl Branch/Commit ID: 2b8146f76595f0c4d8bf692de78b21280162b1d0
	fail-unconnected.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/fail-unconnected.cwl Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
	prep.cwl	https://git.astron.nl/RD/LINC.git Path: workflows/linc_target/prep.cwl Branch/Commit ID: 1e91001f761abbddeb2c9f4528ed4cec41d113f3