From 7fbef0081015ae7eb7b06ac7bc2bf6b9b253271c Mon Sep 17 00:00:00 2001 From: Chris Rosenthal Date: Thu, 26 Sep 2024 10:54:26 -0700 Subject: [PATCH] output cutadapt fastqs to output dir --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 2a2db73..6ba27ae 100644 --- a/main.nf +++ b/main.nf @@ -137,7 +137,7 @@ process cutadapt { tuple val(sampleid), path("${sampleid}_R1_trimmed.fq.gz"), path("${sampleid}_R2_trimmed.fq.gz") path("counts.csv") - publishDir "${params.output}/cutadapt/${sampleid}/", overwrite: true, mode: 'copy', pattern: '*.{json,tsv,csv}' + publishDir "${params.output}/cutadapt/${sampleid}/", overwrite: true, mode: 'copy' """ cutadapt ${cutadapt_params_str} -o ${sampleid}_R1_trimmed.fq.gz -p ${sampleid}_R2_trimmed.fq.gz R1.fq.gz R2.fq.gz --json=${sampleid}.cutadapt.json --report=minimal > ${sampleid}.cutadapt.tsv