From aaefa600a2587c118bec7f93f0b3a4d3f80962f5 Mon Sep 17 00:00:00 2001 From: kiei-rz Date: Wed, 4 Dec 2024 16:22:25 +0100 Subject: [PATCH] Fix stub run trimmomatic --- modules/nf-core/trimmomatic/main.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf index 13fe8b6ee7a..ae8e9aad9d4 100644 --- a/modules/nf-core/trimmomatic/main.nf +++ b/modules/nf-core/trimmomatic/main.nf @@ -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" } 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" } """