Skip to content

add seq_type to anarcii module - #12813

Open
mapo9 wants to merge 4 commits into
nf-core:masterfrom
mapo9:anarcii_seqtype
Open

add seq_type to anarcii module#12813
mapo9 wants to merge 4 commits into
nf-core:masterfrom
mapo9:anarcii_seqtype

Conversation

@mapo9

@mapo9 mapo9 commented Aug 26, 2026

Copy link
Copy Markdown
Contributor

nf-core/modules pull request

PR checklist

Adds seq_type as an input to anarcii, passed to the tool's -t flag.

-t/--seq_type defaults to antibody. The module never sets it, so numbering other input needs an ext.args override that is easy to omit, and getting it wrong is silent: ANARCII returns unnumbered chain F instead of erroring.
That's why I consider that the flag should be part of the nf-core modules. Also, AFAIK no pipeline uses it yet (mine will very soon :D), so PR won't break anything

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines. (I hope, unsure if meta-maps are required for all inputs??)
  • Add a resource label
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

@mapo9
mapo9 marked this pull request as draft August 26, 2026 09:59
@mapo9
mapo9 marked this pull request as ready for review August 26, 2026 10:06
mapo9 and others added 2 commits August 26, 2026 11:15
ANARCII's Score column drifts with thread count, so a whole-file md5 is not
portable across machines and failed in CI.

@CaroAMN CaroAMN left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM :)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants