Staphtyper module compilation error

[Kiratrea]

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

• file : /home/grege/anaconda3/envs/bactopia-dev/share/bactopia-3.0.2/./workflows/../lib/nf/bactopia_tools.nf
• cause: Unexpected input: '{\n // Default to Bakta faa\n faa = "${base_dir}/${PATHS['faa']}/bakta/${sample}.faa"\n gff = "${base_dir}/${PATHS['faa']}/bakta/${sample}.gff3"\n if (!file("${faa}").exists() && !file("${faa}.gz").exists()) {\n // Fall back on Prokka\n faa = "${base_dir}/${PATHS['faa']}/prokka/${sample}.faa"\n gff = "${base_dir}/${PATHS['faa']}/bakta/${sample}.gff"\n }\n\n if (file("${fna}.gz").exists() && file("${faa}.gz").exists() && file("${gff}.gz").exists()) {\n return tuple([id:sample, is_compressed:true], [file("${fna}.gz")], [file("${faa}.gz")], [file("${gff}.gz")])\n } else if (file(fna).exists() && file(faa).exists() && file(gff).exists() {\n return tuple([id:sample, is_compressed:false], [file("${fna}")], [file("${faa}")], [file("${gff}")])\n }\n }' @ line 188, column 5. } else if (extension == 'fna_faa') { ^

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]

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]

Wahoo, looks great! Thanks!

[rpetit3]

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