Explore Workflows

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

Path: tests/count-lines1-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

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

Path: tests/wf/mut.cwl

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de

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

Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl

Branch/Commit ID: 6ccec9c5c5bc9fb4e75ca0b9cc22d13df9ffb815

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

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

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de

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: 12c29f88855329192bfff977f046990031f04931

Reverse the lines in a document, then sort those lines.

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

Path: cwltool/schemas/v1.0/v1.0/revsort.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9

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

Path: definitions/pipelines/detect_variants_mouse.cwl

Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b

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

Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

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

Path: tests/io-int-default-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: 64e85970dbecba89c3380ab285c108d221e76fe6