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Graph	Name	Retrieved From	View
	Trim Galore RNA-Seq pipeline single-read strand specific Note: should be updated 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-end 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. 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/trim-rnaseq-se-dutp.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	SetTelescopeEfficiency Derive (or set) an overall efficiency parameter to the telescope throughput due to variations of the optical throughput. Allow for dependencies on off-axis angle and wavelength.	https://github.com/gammasim/workflows.git Path: workflows/SetTelescopeEfficiency.cwl Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
	Cell Ranger Aggregate (RNA+ATAC) Cell Ranger Aggregate (RNA+ATAC) Combines outputs from multiple runs of “Cell Ranger Count (RNA+ATAC)” pipeline. The results of this workflow are primarily used in “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipeline.	https://github.com/datirium/workflows.git Path: workflows/cellranger-arc-aggr.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	Non-Coding Bacterial Genes	https://github.com/ncbi/pgap.git Path: bacterial_noncoding/wf_bacterial_noncoding.cwl Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
	Trim Galore RNA-Seq pipeline paired-end strand specific Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) RNA-Seq basic analysis for a pair-end 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-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. 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 files 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/trim-rnaseq-pe-dutp.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	umi molecular alignment workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
	tt_kmer_compare_wnode Pairwise comparison	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_compare_wnode.cwl Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6
	SetLightGuideEfficiency Set light guide efficiency as function of wavelength and incident angle.	https://github.com/gammasim/workflows.git Path: workflows/SetLightGuideEfficiency.cwl Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
	kf_STAR_Solo_10x_alignment_wf.cwl	https://github.com/kids-first/kf-dev-single-cell-rna.git Path: workflows/kf_STAR_Solo_10x_alignment_wf.cwl Branch/Commit ID: 8c1d2315ad46fe0a30bf618e108e55b0263c7c6d
	workflow_input_sf_expr_array.cwl	https://github.com/common-workflow-language/cwl-utils.git Path: testdata/workflow_input_sf_expr_array.cwl Branch/Commit ID: b76b039edb62dea76c43f173848cdc57e4b4aab7