Explore Workflows

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

Graph	Name	Retrieved From	View
	Apply filters to VCF file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
	trnascan_wnode and gpx_qdump combined	https://github.com/ncbi/pgap.git Path: bacterial_trna/wf_scan_and_dump.cwl Branch/Commit ID: 8ea3637b0f11eac1ea5599c41d74e00d85fb778d
	assm_assm_blastn_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c
	bacterial_orthology_cond	https://github.com/ncbi/pgap.git Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl Branch/Commit ID: 2afb5ebafd1353ba063cc74ee9a7eaf347afce5c
	wgs alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/wgs.cwl Branch/Commit ID: 3ee63d8757c341ca98b3b46ec4782862ad19b710
	extract_file_with_index.cwl	https://github.com/NCI-GDC/aliquot-maf-cwl.git Path: vcf-to-aliquot-maf/subworkflows/extract_file_with_index.cwl Branch/Commit ID: af9e756697f29b082790b65f129a6434fd5c4980
	workflow-ebisearch.cwl	https://github.com/ebi-jdispatcher/webservice-cwl.git Path: workflows/workflow-ebisearch.cwl Branch/Commit ID: 88b9948c4977ca90ab5ceb391b2235043135480d
	Chipseq alignment with qc and creating homer tag directory	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/chipseq.cwl Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
	Whole genome alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_wgs.cwl Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268
	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: 4a80f5b8f86c83af39494ecc309b789aeda77964