Explore Workflows

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Graph	Name	Retrieved From	View
	kmer_cache_store	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_cache_store.cwl Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
	exome alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/exome.cwl Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4
	Filter differentially expressed genes from DESeq for Tag Density Profile Analyses Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.	https://github.com/datirium/workflows.git Path: workflows/filter-deseq-for-heatmap.cwl Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
	Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/pvacseq.cwl Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4
	rnaseq-se-dutp.cwl Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.	https://github.com/Barski-lab/workflows.git Path: workflows/rnaseq-se-dutp.cwl Branch/Commit ID: e89b2c17aa5efccef6ca424dec5a0a021bd8d20c
	blastp_wnode_struct	https://github.com/ncbi/pgap.git Path: task_types/tt_blastp_wnode_struct.cwl Branch/Commit ID: a2d6cd4c53bf3501f6bd79edebb7ca30bba8456f
	js-expr-req-wf.cwl#wf	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl Branch/Commit ID: d7cd45f7072960d264962ecc5a04d7c219f65c06 Packed ID: wf
	revsort.cwl Reverse the lines in a document, then sort those lines.	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/revsort.cwl Branch/Commit ID: 2a8af96d334e6979cb00af4569581d192d43ce41
	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: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9
	Unaligned bam to sorted, markduped bam	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/align_sort_markdup.cwl Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0