Extract meryl+merqury subworkflow into modules - Githubissues

nf-core / genomeqc

Compare the quality of multiple genomes, along with their annotations.

https://nf-co.re/genomeqc

MIT License

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Extract meryl+merqury subworkflow into modules #71

Open stephenturner opened 3 weeks ago

stephenturner commented 3 weeks ago

PR #63 brings in changes that allow optionally passing in reads to support quality metrics that require them, such as using kmer counts from raw sequencing data to evaluate accuracy and completeness using Merqury (#42). @GallVp added a nice suggestion in #63 to extract a subworkflow into nf-core/modules that could be used across workflows.

See also:

https://github.com/nf-core/modules/issues/6905 (new subworkflow issue in nf-core/modules -- after this is finished, come back to genomeqc here to use the subworkflow module

Would be great to support the trio mode with parental reads. This is supported by the assemblyqc pipeline. Maybe, we can extract a sub workflow, put it on nf-core/modules so that the two pipelines can benefit from shared development. Please see the workflow on the assemblyqc repo:

https://github.com/Plant-Food-Research-Open/assemblyqc/blob/cec2728d0785d97e0e9493558c83d83d0b48240e/workflows/assemblyqc.nf#L598-L771

Originally posted by @GallVp in https://github.com/nf-core/genomeqc/issues/63#issuecomment-2442810796

stephenturner commented 3 weeks ago

Note to self, useful docs:

Docs: Create a subworkflow: https://nf-co.re/docs/nf-core-tools/subworkflows/create
Docs: Writing nf-core modules and subworkflows: https://nf-co.re/docs/contributing/subworkflows