Release PR for 2.1.0

[jasmezz]

Edit 1: WE WILL IGNORE CONDA CI TEST FAILURES TO THEM BEING A CONDA OVERLAPPING LOCK ERROR RELATED TO NEXTFLOW

Edit 2: Nevermind, we do care and updated Nextflow to 24.10.4 where the above bug is fixed.

Added

• #421 Updated to nf-core template 3.0.2. (by @jfy133)
• #427 AMPcombi now can use multiple other databases for classifications. (by @Darcy220606)
• #428 Added InterProScan annotation workflow to the pipeline. The results are coupled to AMPcombi final table. (by @Darcy220606)
• #429 Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz)
• #433 Updated to nf-core template 3.1.1. (by @jfy133)
• #431 Updated AMPcombi, Macrel, all MMseqs2 modules, MultiQC, Pyrodigal, and seqkit, added --taxa_classification_mmseqs_compressed parameter. (by @jasmezz)
• #438 Updated to nf-core template 3.1.2. (by @jfy133)
• #441 Updated to nf-core template 3.2.0, updated MultiQC. (by @jasmezz and @jfy133)
• #440 Updated Bakta and introduced new parameter --annotation_bakta_hmms. (by @jasmezz)

Fixed

• #427 Fixed the AMP reference database issues reported by users, due to non-ASCII characters. (by @Darcy220606)
• #430 Updated rgi/main module to fix incorrect variable name. (by @amizeranschi and @jasmezz)
• #435 Fixed dependency errors within taxonomy merging scripts, updated the code and output for all three workflows. Bumped to version 0.1.1. (by @Darcy220606)
• #437 Fixed file name error when supplying already preprocessed CARD database for ARG workflow. (by @jasmezz)
• #446 Updated antiSMASH modules to fix apptainer execution. (by @jasmezz and @jfy133)
• #448 Fixed taxonomy merge to work with output from GTDB/SILVA/KALAMARI. (by @Darcy220606)
• #447 Added --annotation_pyrodigal_usespecialstopcharacter parameter to improve AMPlify screening. (by @jasmezz)
• #454 Updated default CPU requirement of ampcombi2/parsetables. (by @jasmezz)

Dependencies

Tool	Previous Version	New Version
AMPcombi	0.2.2	2.0.1
Bakta	1.9.3	1.10.4
InterProScan	-	5.59_91.0
Macrel	1.2.0	1.4.0
MMseqs2	15.6f452	17.b804f
MultiQC	1.24.0	1.27
Pyrodigal	3.3.0	3.6.3
seqkit	2.8.1	2.9.0

Deprecated

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[jasmezz]

I addressed everything except for sharding and the update of the workflow diagram discussed with @mashehu before.
The code changes have to be added via #459 because I cannot push the suggestions directly to dev for some reason. Feel free to approve and merge that PR!

[jasmezz]

Oh and @mashehu, if I specify a more recent minimum Nextflow version in nextflow.config than what the template is using, those part of the CI tests will fail: https://github.com/nf-core/funcscan/actions/runs/13587320992/job/37985088177?pr=459#step:11:103

Leave like this or change back?

• Leave as is: all Nextflow 24.04.2 tests will fail (because >24.10.2 is specified)
• Change back: all conda tests will fail (would require Nextflow >24.10.2)
• Update version in ci.yml to 24.10.2 (would then be different from the template, but fix CI tests)

[mashehu]

tests are more important than linting in this case: so change ci.yml to 24.10.2 (and add it to the lint ignore list in nf-core.yml)

[jfy133]

@jasmezz I've fixed the pending checks (something that had to be changed in the repo settings), I bumped the date for tomorrow, and as it was Matthias who said we should use the later minimal version with linting skip, I've done that too (I realised when reading the comment that the minimal CI version doesn't correspond to the minimal version we specify in nextflow.config so indeed this is better).

[jfy133]

@jasmezz conda is working now but it looks like there are ampcombi snapshot differences in them...

[jfy133]

Only one of the download pipeline is not passing but this is an upstream bug with the CI test not the funcitonality itself (the other test passes)