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1 parent 48ca3de commit 3351c21Copy full SHA for 3351c21
modules/nf-core/bbmap/bbduk/main.nf
@@ -26,15 +26,15 @@ process BBMAP_BBDUK {
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def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
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def contaminants_fa = contaminants ? "ref=$contaminants" : ''
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"""
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- maxmem=\$(echo \"$task.memory\"| sed 's/ GB/g/g')
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bbduk.sh \\
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- -Xmx\$maxmem \\
+ -Xmx${task.memory.toGiga()}g \\
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$raw \\
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$trimmed \\
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threads=$task.cpus \\
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$args \\
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$contaminants_fa \\
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&> ${prefix}.bbduk.log
+
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bbmap: \$(bbversion.sh | grep -v "]")
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