Explore Workflows

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Graph	Name	Retrieved From	View
	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
	hybrid_error_correction.cwl Sub workflow used in the Animal Genome Assembly pipeline by Kazuharu Arakawa (@gaou_ak), CWLized by Tazro Ohta (@inutano)	https://github.com/pitagora-network/DAT2-cwl.git Path: workflow/animal-genome-assembly/hybrid_error_correction.cwl Branch/Commit ID: 0cd20e1be620ae0817a1aa4286d73b78c89809f0
	Nested workflow example	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/nested.cwl Branch/Commit ID: e835bc0487fe42fb330b6222c9be65d18dd81ec9
	Bisulfite alignment and QC	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/bisulfite.cwl Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54