Ensure all tools have relevant critical parameters accessible at pipeline level - Githubissues

nf-core / funcscan

(Meta-)genome screening for functional and natural product gene sequences

https://nf-co.re/funcscan

MIT License

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Ensure all tools have relevant critical parameters accessible at pipeline level #80

Closed jfy133 closed 1 year ago

jfy133 commented 2 years ago

We need to make sure that all (relevant) parameters that a user may want to tweak of a given tool are available to be modifiable by the pipelie user (see deepARG, where this is already added).

Before release we should do a pass to check every tool and insert params where necessary.

Darcy220606 commented 1 year ago

Check parametrs in all modules in the workflows. If checked, either a PR was made or no xtra parametrs required

AMP workflow

[x] Macrel (fna contig min. 1000, but we do not run this function in funcscan)
[x] Amplify (max 200aa)
[x] ampir (min is a ext.parametre - now default: 10aa)
[x] hmmsearch
BGC workflow
[x] antismash
[x] gecco
[x] deepbgc
ARG workflow
[x] AMRFINDERPLUS
[x] Fargene
[x] RGI
[x] abricate
[x] deeparg
Annotations
[x] Prodigal
[x] Prokka
[x] Bakta
Reports
[x] ampcombi
[x] hamronisation
[ ] combgc