I added a new parameter to let the user skip the check if the chosen peptide lengths can be used for all alleles. This may result in an analysis bias if alleles are compared against each other, which is the reason we included the checks and unification in the first place.
I therefore, needed to double check also in the prediction to not throw errors.
Also I deleted one logging line, which may be misinterpreted. The line stated that specific alleles did not yield any predictions, which may happen if the prediction chunk contains only unsupported peptide lengths. Therefore, the allele did in fact yield predictions, but just not for one chunk.
PR checklist
[x] 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/metapep 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).
I added a new parameter to let the user skip the check if the chosen peptide lengths can be used for all alleles. This may result in an analysis bias if alleles are compared against each other, which is the reason we included the checks and unification in the first place.
I therefore, needed to double check also in the prediction to not throw errors.
Also I deleted one logging line, which may be misinterpreted. The line stated that specific alleles did not yield any predictions, which may happen if the prediction chunk contains only unsupported peptide lengths. Therefore, the allele did in fact yield predictions, but just not for one chunk.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).