Explore Workflows

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

Graph	Name	Retrieved From	View
	workflow.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_dispatch/workflow.cwl Branch/Commit ID: b1e1b906fcfb2c0fad8811fb8ab03009282c1d19
	kmer_seq_entry_extract_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad
	Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)	https://github.com/ncbi/pgap.git Path: bacterial_annot/wf_bacterial_annot_pass4.cwl Branch/Commit ID: 5463361069e263ad6455858e054c1337b1d9e752
	exome alignment with qc, no bqsr, no verify_bam_id	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/alignment_exome_nonhuman.cwl Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
	pulsar_timing_prototype_workflow.cwl	https://github.com/tmcantwell/pulsar_timing_prototype.git Path: pulsar_timing_prototype_workflow.cwl Branch/Commit ID: cfbb07cf9d214fff636c305675530748e94b359a
	align_sort_sa	https://github.com/ncbi/pgap.git Path: task_types/tt_align_sort_sa.cwl Branch/Commit ID: 4e2a295bb6c8b4982402ee80538a0cdb8ee6b6dd
	MoveData-workflow.cwl	https://github.com/NAL-i5K/Organism_Onboarding.git Path: MoveData-workflow.cwl Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
	Apply filters to VCF file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/germline_filter_vcf.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d
	Detect Variants workflow	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/detect_variants_nonhuman.cwl Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
	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: 09267e79fd867aa68a219c69e6db7d8e2e877be2