Explore Workflows

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

Graph	Name	Retrieved From	View
	blastp_wnode_struct	https://github.com/ncbi/pgap.git Path: task_types/tt_blastp_wnode_struct.cwl Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6
	count-lines11-null-step-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/count-lines11-null-step-wf.cwl Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
	format_rrnas_from_seq_entry	https://github.com/ncbi/pgap.git Path: task_types/tt_format_rrnas_from_seq_entry.cwl Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
	Deprecated. Single-cell Differential Expression Deprecated. Single-cell Differential Expression =============================================== Runs differential expression analysis for a subset of cells between two selected conditions.	https://github.com/datirium/workflows.git Path: workflows/sc_diff_expr.cwl Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
	metrics.cwl	https://github.com/NCI-GDC/gdc-dnaseq-cwl.git Path: workflows/dnaseq/metrics.cwl Branch/Commit ID: 8edf6a5e4e7790434ad0742e50d0c97a5d0bb846
	scatter-valuefrom-wf3.cwl#main	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl Branch/Commit ID: 7bfe73a708dbf31d037303bb5a8fed1a79984b0f Packed ID: main
	umi molecular alignment workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/molecular_qc.cwl Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
	wgs alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/tumor_only_wgs.cwl Branch/Commit ID: 789267ce0e3fed674ea5212a562315218fcf1bfc
	sum-wf.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/sum-wf.cwl Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2
	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: 3fc68366adb179927af5528c27b153abaf94494d