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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
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
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: 0cd9f79ba7ERROR ~ Module compilation error
} 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
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