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Graph	Name	Retrieved From	View
	Cut-n-Run pipeline paired-end Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed	https://github.com/datirium/workflows.git Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: 2c486543c335bb99b245dfe7e2f033f535efb9cf
	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: 9bf0aa495735f8081bb5870cb32fc898b9e6eb22
	FASTQ Vector Removal This workflow clean up vectros from fastq files	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/File-formats/remove-fastq-reads-from-blast.cwl Branch/Commit ID: 6eb7fec3bd018addf02bb3285cb56d9453319d5d
	broad-best-practice-data-pre-processing-workflow-4-1-0-0_decomposed.cwl	https://github.com/svonworl/Broad-Best-Practice-Data-pre-processing-CWL1.0-workflow.git Path: broad-best-practice-data-pre-processing-workflow-4-1-0-0_decomposed.cwl Branch/Commit ID: fe43d13c174816704f1d7941dc8cb5fce358c0de
	Cut-n-Run pipeline paired-end Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed	https://github.com/datirium/workflows.git Path: workflows/trim-chipseq-pe-cut-n-run.cwl Branch/Commit ID: 8a92669a566589d80fde9d151054ffc220ed4ddd
	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: subworkflows/heatmap-prepare.cwl Branch/Commit ID: 02ffbbd7eb8e06bfb759edea440f78bdc8bb2631
	indexing_bed	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl Branch/Commit ID: a4a3547b9790e99a58424a0dfcb4e467a7691d6a
	extract_readgroups_bam_http.cwl	https://github.com/nci-gdc/gdc-dnaseq-cwl.git Path: workflows/bamfastq_align/extract_readgroups_bam_http.cwl Branch/Commit ID: 0495e3095182b2e1b4d6274833b3d2ce30347a4e
	allele-alignreads-se-pe.cwl Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.	https://github.com/datirium/workflows.git Path: subworkflows/allele-alignreads-se-pe.cwl Branch/Commit ID: 9bf0aa495735f8081bb5870cb32fc898b9e6eb22
	wffail.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/wffail.cwl Branch/Commit ID: 20d664eff23e59aa57908345bfdb1ceeab3438f2