bactopia / bactopia

A flexible pipeline for complete analysis of bacterial genomes
https://bactopia.github.io
MIT License
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Staphtyper module compilation error #503

Closed Kiratrea closed 1 month ago

Kiratrea commented 6 months ago

Hello, after successfully processing all my samples I have been trying to use the staphtyper workflow. Each time I come across this error. I can't seem to figure out what is causing the unexpected input, could my file structure be part of the issue?

N E X T F L O W ~ version 23.10.1 Launching /home/grege/anaconda3/envs/bactopia-dev/share/bactopia-3.0.2/main.nf [distracted_ptolemy] DSL2 - revision: 0cd9f79ba7 ERROR ~ Module compilation error

1 error

-- Check script 'anaconda3/envs/bactopia-dev/share/bactopia-3.0.2/./workflows/bactopia-tools.nf' at line: 9 or see '.nextflow.log' file for more details

Here is the nextflow log file .nextflow.log

rpetit3 commented 6 months ago

Hi @Kiratrea

Thank you for bringing this to my attention! It is now fixed (https://github.com/bactopia/bactopia/commit/cfd4c125fde9e76fe2ff2b28bbe746382f8f8202) and available from the dev version.

Cheers, Robert

Kiratrea commented 6 months ago

Wahoo, looks great! Thanks!

rpetit3 commented 1 month ago

Hi @Kiratrea

I've released a new version of Bactopia (https://github.com/bactopia/bactopia/releases/tag/v3.1.0). I think you will be interested in the new sccmec tool I've added.

I will go ahead and close, Robert