To fix before next releases

[maxulysse]

Description of feature

I think we can have some easy win before the release and gain more global coherence with other nf-core pipelines:

• lib/ folder -> move the function in subworkflows/local/utils_nfcore_raredisease_pipeline
• all local modules should be in their own modules/local/whatever/main.nf
• subworkflows/local -> move each script in its own subworkflows/whatever/whichever/main.nf
• remove any unused modules/subworkflows/functions
• test_full is test without stub

For the next release:

• tests for local modules and local subworkflows, and pipeline
• profile test to run without stub (remove annotation and just use 1 variant caller)
• add alternate steps to start pipeline
• test with sentieon
• real full_size test (use same data as germline sarek (1 sample) and skip annotation)
• Use igenomes for the full_size test

[fellen31]

A bit along the same lines, there's a few local modules (add_most_severe_consequence, add_most_severe_pli) and subworkflows (annotate_consequence_pli, annotate_repeat_expansions, rank_variants) that are shared now between raredisease and nallo. Do you think it would be okay/a good idea to make these nf-core modules/subworkflows instead, to share the maintenance?

[maxulysse]

A bit along the same lines, there's a few local modules (add_most_severe_consequence, add_most_severe_pli) and subworkflows (annotate_consequence_pli, annotate_repeat_expansions, rank_variants) that are shared now between raredisease and nallo. Do you think it would be okay/a good idea to make these nf-core modules/subworkflows instead, to share the maintenance?

Of course <3