Explore Workflows

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

Graph	Name	Retrieved From	View
	Bisulfite alignment and QC	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/bisulfite.cwl Branch/Commit ID: cc3e7f1ccfdc7101c22bf88792608504eea7d53a
	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: ee66d03be8a7fd61367db40c37a973ff55ece4da
	Detect DoCM variants	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: 5cb188131f786ed33156e2f0e3dd63ab9c04245d
	DiffBind - Differential Binding Analysis of ChIP-Seq Peak Data Differential Binding Analysis of ChIP-Seq Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4.	https://github.com/datirium/workflows.git Path: workflows/diffbind.cwl Branch/Commit ID: 564156a9e1cc7c3679a926c479ba3ae133b1bfd4
	Bismark Methylation SE Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).	https://github.com/datirium/workflows.git Path: workflows/bismark-methylation-se.cwl Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
	kmer_ref_compare_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: e71779665f42fcf34601b0f65e030bb0dd47fa79
	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: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
	Detect DoCM variants	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: 76a35e7d885790f30559beb31f3b58770e343afd
	xenbase-sra-to-fastq-pe.cwl	https://github.com/datirium/workflows.git Path: subworkflows/xenbase-sra-to-fastq-pe.cwl Branch/Commit ID: 9b4dc225c537685b9c9a32d931d3892d20953dd7
	mut3.cwl	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/mut3.cwl Branch/Commit ID: 4df56e95e6fceab69e677b539f3532cbf5946197