Fix filters with --input_fasta

d4straub commented 1 year ago

Closes https://github.com/nf-core/ampliseq/issues/629

Also added verbose error message if ASV length or codon filter remove all ASVs. rRNA filter had such an error already.

Fixed:

nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --max_len_asv 265
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --filter_ssu bac
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --filter_codons --orf_end 3
nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --filter_codons --orf_end 30 --max_len_asv 265 --filter_ssu bac

Will not fix: nextflow run ampliseq -profile test_fasta,singularity --outdir results_fasta -resume --vsearch_cluster therefore no VSEARCH clustering will be available with fasta file input. If need be that can be fixed in another PR.

PR checklist

[x] This comment contains a description of changes (with reason).
[x] 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/ampliseq branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 1 year ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 928beeb

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

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d4straub commented 1 year ago

Thanks for the approval but I attempt to fix test_fasta with all functionality, so I will add a few more commits ;)

erikrikarddaniel commented 1 year ago

I had two minutes before a meeting... ;-)

d4straub commented 1 year ago

Alright, I think all is fine.

nf-core / ampliseq