Explore Workflows

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

Graph	Name	Retrieved From	View
	SV filtering workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/filter_sv_vcf.cwl Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21
	count-lines7-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/count-lines7-wf.cwl Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
	facets-suite-workflow.cwl Workflow for running the facets suite workflow on a single tumor normal pair Includes handling of errors in case execution fails for the sample pair	https://github.com/mskcc/pluto-cwl.git Path: cwl/facets-suite-workflow.cwl Branch/Commit ID: 5cad957fec135aa55ca8d588372db0557ca1cad5
	kmer_cache_retrieve	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_cache_retrieve.cwl Branch/Commit ID: 92118627c800e4addb7e29b9dabcca073a5bae71
	tRNA_selection.cwl	https://github.com/proteinswebteam/ebi-metagenomics-cwl.git Path: tools/tRNA_selection.cwl Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193
	Vcf concordance evaluation workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/vcf_eval_concordance.cwl Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
	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: 60854b5d299df91e135e05d02f4be61f6a310fbc
	Bismark Methylation - pipeline for BS-Seq data analysis 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: 60854b5d299df91e135e05d02f4be61f6a310fbc
	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: 3d280a2a4b4f1560f56991086f712fa22ddc3364
	align_merge_sas	https://github.com/ncbi/pgap.git Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: 9144d08fa7f4e852498761481dceab477167fa65