Explore Workflows

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: 7518b100d8cbc80c8be32e9e939dfbb27d6b4361

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

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb

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

Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl

Branch/Commit ID: f997d13af87216e9b5048c732a511053c7ba714c

Allele specific RNA-Seq (using vcf) single-read workflow

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

Path: workflows/allele-vcf-rnaseq-se.cwl

Branch/Commit ID: d6ec0dee61ef65a110e10141bde1a79332a64ab0

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

Path: tests/count-lines11-wf.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 0e8110083bad6ea98fc487aa262953a6c5e010b5

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

Path: tests/wf/nested.cwl

Branch/Commit ID: 0e98de8f692bb7b9626ed44af835051750ac20cd

Modified from https://github.com/kids-first/kf-somatic-workflow/blob/master/sub_workflows/prepare_reference.cwl

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/bwa_index.cwl

Branch/Commit ID: b62c7bfcf5eb7ac3c1ed06879200fdf5db947e4b

Workflow to convert a RDF file to the HDT format and GZIP compress it for long term storage

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_toHDT_compression.cwl

Branch/Commit ID: 60fafdfbec9b39c860945ef4634e0c28cb5e976c

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: 0db44e3c9805a070564f954222efff71cd791b70