Closed tillenglert closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 6ac038c
+| ✅ 159 tests passed |+
!| ❗ 12 tests had warnings |!
@nf-core-bot fix linting
Now I was/am a bit confused (and don't remember), what do you mean exactly with "mouse alleles are no findable"?
OK, .... is it that epytope returns 8-13 with the supported_length
function (https://github.com/KohlbacherLab/epytope/blob/28d70d4074194b5e604dd38f0fc973dce2e37ded/epytope/EpitopePrediction/PSSM.py#L123), but not all of those lengths are actually supported for each allele? Is this different for the other tools?
OK, .... is it that epytope returns 8-13 with the
supported_length
function (https://github.com/KohlbacherLab/epytope/blob/28d70d4074194b5e604dd38f0fc973dce2e37ded/epytope/EpitopePrediction/PSSM.py#L123), but not all of those lengths are actually supported for each allele? Is this different for the other tools?
Yes exactly, for syfpeithi the models which are used, can be found at https://github.com/KohlbacherLab/epytope/tree/main/epytope/Data/pssms/syfpeithi/mat Most models support lengths of 9 and 10, some also 8 or 11 but 12 and 13 are actually never "supported" I guess you can throw the peptide lengths of 8-13 to syfpeithi but it will not return any predictions? Maybe epytope has not implemented all models which are supported at the website? In Epytope syfpeithi is internally handled, while the other tools are actually called externally, so I guess in this case the output will be more sensible? Still in cases like this the output of the prediction need to be checked to not run into mathematical errors later on (for syfpeithi this is already implemented in PR: https://github.com/nf-core/metapep/pull/75) for the others this needs to be implemented at post processing, if more steps are added.
I updated the version of the Epytope upgrade to the newest version (3.3.1.) This version fixes the mouse alleles and GitHub CI tests on the home repo should work again.
As the mouse alleles are no findable again by epytope I discovered that most peptide lengths are not supported for syfpeithi (issue: #74). Therefore I reduced the lengths of the peptide to 9 to match the syfpeithi models.
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).