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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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FORMAT_PPLACETAX fails because of missing str_split function #808

Open jkibilds opened 3 days ago

jkibilds commented 3 days ago

After phylogenetic placement, the pipeline fails at FORMAT_PPLACETAX with this error:


  Error in str_split(temp$taxopath, ";") : 
    could not find function "str_split"
  Execution halted```

This task completes successfully if I add `library(stringr)` at the beginning of `.command.sh` file in the working directory of the failed task and then launch `.command.run`. This fixes the problem, since the missing `str_split` function can be found in stringr R package. 

Required fix: add `library(stringr)` at the beginning of [modules/local/format_pplacetax.nf](https://github.com/nf-core/ampliseq/blob/master/modules/local/format_pplacetax.nf)

[Slack Message](https://nfcore.slack.com/archives/CEA7TBJGJ/p1732831200432689?thread_ts=1732831200.432689&cid=CEA7TBJGJ)
erikrikarddaniel commented 3 days ago

Thanks for reporting. This is a bit strange, since the test passes but the code does not look like it should work. I'll fix this in the dev branch so it should be in the next release.