Explore Workflows

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

Graph	Name	Retrieved From	View
	Running cellranger count and lineage inference	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/single_cell_rnaseq.cwl Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075
	Build Bowtie indices Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome	https://github.com/datirium/workflows.git Path: workflows/bowtie-index.cwl Branch/Commit ID: 730b40bc403263b724399a952c0f3e2d28f13519
	step-valuefrom5-wf.cwl	https://github.com/common-workflow-language/cwl-v1.2.git Path: tests/step-valuefrom5-wf.cwl Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
	cram_to_bam workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cram_to_bam_and_index.cwl Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
	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: e99e80a2c19682d59947bde04a892d7b6d90091c
	directory.cwl Inspect provided directory and return filenames. Generate a new directory and return it (including content).	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/directory.cwl Branch/Commit ID: d6000d32f6c8fbd26421a2d30d79b28901d58fb0
	Super-enhancer post ChIP-Seq analysis Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)	https://github.com/datirium/workflows.git Path: workflows/super-enhancer.cwl Branch/Commit ID: 4a80f5b8f86c83af39494ecc309b789aeda77964
	filter-pcr-artifacts.cwl DNase-seq - map - Filter PCR Artifacts	https://github.com/alexbarrera/GGR-cwl.git Path: v1.0/map/filter-pcr-artifacts.cwl Branch/Commit ID: 33385c6a820a9d4d18cff6fc3a533ec8e3c11c6e
	exome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome_mouse.cwl Branch/Commit ID: 3f3b186da9bf82a5e2ae74ba27aef35a46174ebe
	env-wf2.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/env-wf2.cwl Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63