Explore Workflows

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

Graph	Name	Retrieved From	View
	hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather	https://github.com/ncbi/pgap.git Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e
	lobSTR-workflow.cwl	https://github.com/common-workflow-language/cwlviewer.git Path: src/test/resources/cwl/lobstr-v1/lobSTR-workflow.cwl Branch/Commit ID: 73d2f7469a1572e6891fe4e6e26021196eb1b3ef
	apolloServer-createOrganism-workflow.cwl	https://github.com/NAL-i5K/Organism_Onboarding.git Path: apolloServer-createOrganism-workflow.cwl Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729
	Subworkflow that runs cnvkit in single sample mode and returns a vcf file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022
	idr.cwl	https://github.com/ncbi/cwl-ngs-workflows-cbb.git Path: workflows/ChIP-Seq/idr.cwl Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419
	workflow-blast-ebeye-pdbe.cwl	https://github.com/ebi-wp/webservice-cwl.git Path: workflows/workflow-blast-ebeye-pdbe.cwl Branch/Commit ID: 5df6b762980b15b0f6389149311b82bdd6dff37d
	workflow-htcondorcern.cwl	https://github.com/reanahub/reana-demo-root6-roofit.git Path: workflow/cwl/workflow-htcondorcern.cwl Branch/Commit ID: 5a1d6cb8c6ef34958972246dbc6e58c267bdc77c
	prefactor_calibrator.cwl	https://git.astron.nl/eosc/prefactor3-cwl.git Path: workflows/prefactor_calibrator.cwl Branch/Commit ID: 6633c39d59a81b9ebf8312450bf50d6a0fe66efa
	genomics-workspace-cds.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_genomicsWorkspace/genomics-workspace-cds.cwl Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945
	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: 7fb8a1ebf8145791440bc2fed9c5f2d78a19d04c