Commit 69c1bb09 authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

Check gff validity (issue : check point prokka)

parent e6fd319d
...@@ -7,11 +7,18 @@ process PROKKA { ...@@ -7,11 +7,18 @@ process PROKKA {
output: output:
tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results
path "PROKKA_${sampleId}/${sampleId}.txt", emit: report path "PROKKA_${sampleId}/${sampleId}.txt", emit: report
path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results
script: script:
""" """
prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus}
rm PROKKA_${sampleId}/*.gbk rm PROKKA_${sampleId}/*.gbk
gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
then
rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
fi
""" """
} }
......
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