olgabot/infernal cmSCAN not search

[olgabot]

Turns out I had read the INFERNAL documentation wrong and was using cmsearch for annotating RNA-seq reads, but we should be using cmscan instead.

• cmsearch - Search a covariance model against a sequence database.
• cmscan - Search a sequence against a covariance model database.

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 necessary, also make a PR on the nf-core/predictorthologs branch on the nf-core/test-datasets repo
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
• [ ] Make sure your code lints (nf-core lint .).
• [ ] Documentation in docs is updated
• [ ] CHANGELOG.md is updated
• [ ] README.md is updated

Learn more about contributing: CONTRIBUTING.md

[olgabot]

The only failures are downloading refseq which is allowed to fail, and a nextflow fluke

[pranathivemuri]

so any pipelines currently running are actually not searching for the noncoding sequences correctly?

[olgabot]

so any pipelines currently running are actually not searching for the noncoding sequences correctly?

Yes, that's correct