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Fix stub run trimmomatic #7160

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Fix stub run trimmomatic #7160

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10 changes: 5 additions & 5 deletions modules/nf-core/trimmomatic/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -50,12 +50,12 @@ process TRIMMOMATIC {
def prefix = task.ext.prefix ?: "${meta.id}"

if (meta.single_end) {
output_command = "echo '' | gzip > ${prefix}.SE.paired.trim.fastq.gz"
output_command = "echo '' | gzip > ${prefix}.SE.paired.trim.fastq.gz\n"
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@SPPearce SPPearce Dec 5, 2024 •
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Not sure it needs the explicit line break at the last entry does it (same with the paired end underneath)?

} else {
output_command = "echo '' | gzip > ${prefix}.paired.trim_1.fastq.gz"
output_command = "echo '' | gzip > ${prefix}.paired.trim_2.fastq.gz"
output_command += "echo '' | gzip > ${prefix}.unpaired.trim_1.fastq.gz"
output_command += "echo '' | gzip > ${prefix}.unpaired.trim_2.fastq.gz"
output_command = "echo '' | gzip > ${prefix}.paired.trim_1.fastq.gz\n"
output_command += "echo '' | gzip > ${prefix}.paired.trim_2.fastq.gz\n"
output_command += "echo '' | gzip > ${prefix}.unpaired.trim_1.fastq.gz\n"
output_command += "echo '' | gzip > ${prefix}.unpaired.trim_2.fastq.gz\n"
}

"""
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