funcscan
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nf-core
(Meta-)genome screening for functional and natural product gene sequences
### Description of feature Currently, some modules take in `.fna` as an input rather than taking in `.faa` as an input from the annotation tool assigned. This might create diffrerences...
### Description of the bug Benchmarking tests showing resource values are suboptimal when applied to full-size modern data. We should increase resources to reduce the numbers of retries and resumes...
### Description of feature See description on nf-test [here](https://hackmd.io/@Fe-DlBDORpeApqPrKRTlbA/SJVrM7uHh#/) See bitesize talk on nf-test implementation [here](https://www.youtube.com/watch?v=MuwluoKFnwM) Modules in this pipeline which will need to have nf-test implemented: - [x] abricate/run...
### Description of feature [Resfinder](https://github.com/nf-core/modules/tree/master/modules/nf-core/resfinder/run) was just added to modules – let's include it in funcscan!
pharokka (https://github.com/gbouras13/pharokka) is a tool used to functionally annotate phage sequences. It is similar to its bacterial counterparts (Prokka and Bakta). ```[tasklist] ### Tasks - [ ] https://github.com/nf-core/modules/issues/4619 - [...
### Description of feature Optimize [this usage section](https://nf-co.re/funcscan/1.1.3/docs/usage#antismash-1) in the docs: - Clarify what is necessary for the user to prepare for `--bgc_antismash_databases` and `--bgc_antismash_installationdirectory` parameters. - Make clear what...
### Description of feature e.g. Prokka is now [supported](https://multiqc.info/modules/prokka/)
### Description of feature Originating from e.g. metatdenovo and mag pipelines. This would be very helpful for me as I run those pipelines and would like to keep the ORF...
Version `2.14.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
### Description of the bug AMPLIFY_PREDICT fails on **some** protein sequences. The issue is discussed on slack [here](https://nfcore.slack.com/archives/C02K5GX2W93/p1714681983734489). Two input sequences for which AMPLIFY_PREDICT fails/passes are [available on Slack](https://nfcore.slack.com/archives/C02K5GX2W93/p1714722105261119?thread_ts=1714681983.734489&cid=C02K5GX2W93). Pyrodigal...
