Explore Workflows

https://github.com/kids-first/kf-alignment-workflow.git

Path: dev/pilot-run/worklflows/kfdrc_alignment_pipeline.cwl

Branch/Commit ID: d4e818c8b9bf56c83694639aa542bb5c1a174f7d

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/wf-loadContents3.cwl

Branch/Commit ID: c7c97715b400ff2194aa29fc211d3401cea3a9bf

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

This WPS workflow is designed to process ERA5 data, which is usually gathered as two sets of meteorological input grib files, atmosphere (3D data) and surface (2D data). This workflow does not include the geogrid step, that will need to be run separately. Required Inputs: * geo_em* input files (generated by geogrid) * 2 VTables, atmosphere and surface * 2 sets of Grib files, atmosphere and surface * 2 ungrib namelist files, atmosphere and surface * 1 metgrid namelist file Returns: * met_em* files for a single WRF simulation

https://github.com/UoMResearchIT/wrf_emep_cwl_linear_workflow.git

Path: workflows/wps_workflow.cwl

Branch/Commit ID: 70c6a6016eeb4434a3ad82af7908b83d4ea37ce7

this is a placeholder for a missing acceptance workflow.

https://github.com/gammasim/workflows.git

Path: workflows/AcceptParameterWorkflowMissing.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7

https://github.com/common-workflow-language/user_guide.git

Path: src/_includes/cwl/workflows/scatter-workflow.cwl

Branch/Commit ID: 588a8d368e90449f111d9b2581d4ba57039836d4

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c

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: d76110e0bfc40c874f82e37cef6451d74df4f908

https://github.com/BerndDoser/Spherinator.git

Path: streamflow/hipster.cwl

Branch/Commit ID: 34cce5b7986a0b130b661804a7bc67176b1fb6ad