Explore Workflows

Devel version of AltAnalyze Iterative Clustering and Guide-gene Selection =========================================================================

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: 4a44218a713aecc488359be275409414ae8c1434

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: ebbf23764ede324cabc064bd50647c1f643726fa

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

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

Branch/Commit ID: 7c7615c44b80f8e76e659433f8c7875603ae0b25

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

Path: cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b

Perform taxonomic identification tasks on an input genome

https://github.com/ncbi/pgap.git

Path: taxcheck.cwl

Branch/Commit ID: 8af4e2aabf43d5e3c7162efae4ad4649df5601e2

https://github.com/ncbi/pgap.git

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: cd97086739ae5988bab09b05e9259675c4b6bce6

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines11-null-step-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7