Explore Workflows

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Graph	Name	Retrieved From	View
	Detect DoCM variants	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622
	exome alignment and germline variant detection	https://github.com/apaul7/cancer-genomics-workflow.git Path: definitions/subworkflows/germline_detect_variants.cwl Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
	Bismark Methylation PE 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-pe.cwl Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
	count-lines9-wf.cwl	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl Branch/Commit ID: 4700fbee9a5a3271eef8bc9ee595619d0720431b
	cluster_blastp_wnode and gpx_qdump combined	https://github.com/ncbi/pgap.git Path: task_types/tt_cluster_and_qdump.cwl Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
	downsample unaligned BAM and align	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
	allele-process-reference.cwl	https://github.com/datirium/workflows.git Path: subworkflows/allele-process-reference.cwl Branch/Commit ID: 09c08f858e91c4cfd387067f07445722ac7e18aa
	umi molecular alignment workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
	count-lines8-wf-noET.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/count-lines8-wf-noET.cwl Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9
	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: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375