Explore Workflows

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

Graph	Name	Retrieved From	View
	count-lines13-wf.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/count-lines13-wf.cwl Branch/Commit ID: 4fe434e969c93c94b690ba72db295d9d52a6f576
	pipeline-pe.cwl ATAC-seq pipeline - reads: PE	https://github.com/Duke-GCB/GGR-cwl.git Path: v1.0/ATAC-seq_pipeline/pipeline-pe.cwl Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
	03-map-pe-blacklist-removal.cwl ATAC-seq 03 mapping - reads: PE - blacklist removal	https://github.com/Duke-GCB/GGR-cwl.git Path: v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl Branch/Commit ID: 67e8ccd5abddbd9e27f23ceeb95536fecf792d93
	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: 104059e07a2964673e21d371763e33c0afeb2d03
	tt_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_blastn_wnode.cwl Branch/Commit ID: 75ea689c0a8c9902b4598b453455857cb08e885a
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
	scatter-wf4.cwl#main	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/scatter-wf4.cwl Branch/Commit ID: 639229b1159cf484e70e52da10194561b3fad719 Packed ID: main
	Run pindel on provided region	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/pindel_region.cwl Branch/Commit ID: 3b6d0475c80f5e452793a46a38ee188742b86595
	workflow1.cwl	https://github.com/petehague/stoa.git Path: actions/workflow1.cwl Branch/Commit ID: 1bd30c533e4a66da5cbfe531bdac28fcb310f253
	assembly.cwl	https://github.com/vetscience/Assemblosis.git Path: Run/assembly.cwl Branch/Commit ID: 5b9df25ccfd1df3e9fc9a07f48a38b0763039279