Explore Workflows

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

Graph	Name	Retrieved From	View
	workflow.cwl	https://github.com/52North/testbed16-jupyter-notebooks.git Path: workflow_water_masks/workflow.cwl Branch/Commit ID: 56e89ba5babd93134012f77a63027a7a2f65b927
	simple_two_step.cwl	https://github.com/ncbi/cwl-demos.git Path: blast-pipelines/simple_two_step.cwl Branch/Commit ID: 342d1669431d15c8a27589e4c22a91a05033b56c
	workflow.cwl	https://github.com/NAL-i5K/Organism_Onboarding.git Path: flow_create_genomics-workspace_yml/flow_create_yml/workflow.cwl Branch/Commit ID: 3aabbb0f6635bb9354ad52f616ab7cfc61848eb6
	02-trim-se.cwl RNA-seq 02 trimming - reads: SE	https://github.com/alexbarrera/GGR-cwl.git Path: v1.0/RNA-seq_pipeline/02-trim-se.cwl Branch/Commit ID: 4636f2c1a8bcfceeb4b3596ee29e9c06311ed4a1
	Apply filters to VCF file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: b465f0da2806ddb6df481409541d13288ccb40ec
	Prepare user input Prepare user input for NCBI-PGAP pipeline	https://github.com/ncbi/pgap.git Path: prepare_user_input2.cwl Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
	Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass2.cwl Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b
	Unaligned BAM to BQSR and VCF	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl Branch/Commit ID: 8eb189a4a34dc8cd86380685f814c79a444a7601
	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: a0b22644ca178b640fb74849d23b7c631022f0b5
	grep-and-count-for-figure-1.cwl	https://github.com/manabuishii/cwl-samples.git Path: grep-and-count-for-figure-1.cwl Branch/Commit ID: 68e0eb6d95f26b1279262485dbefc440c06fc5f9