The CI tests for conda are failing. The reasons are:
The PRODIGAL module produces a slightly different output (proteins.tsv.gz). This results in changed tables in following modules.
MHCNuggets produces small rounding differences, which lead to different predictions in these tests, and the prediction log is changed due to a changed path within the file.
I tried to keep the tests, but accessing which profile is run within the test is really time intensive compared to the expected usage of conda (which is either way not recommended).
Therefore for now, I would turn off CI testing using conda.
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/metapep branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core pipelines 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).
The CI tests for conda are failing. The reasons are:
The
PRODIGALmodule produces a slightly different output (proteins.tsv.gz). This results in changed tables in following modules.MHCNuggetsproduces small rounding differences, which lead to different predictions in these tests, and the prediction log is changed due to a changed path within the file.I tried to keep the tests, but accessing which profile is run within the test is really time intensive compared to the expected usage of conda (which is either way not recommended).
Therefore for now, I would turn off CI testing using conda.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).