From d0a1cbb703a130c19f6796c3fce24fbe7dfce789 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 18 Feb 2022 15:38:05 +0100 Subject: [PATCH] fix fastp to allow exporting of only `*.merged.fastq.gz` (#1325) * fix: remove left-over unnecessary code * Update main.nf * Update meta.yml --- modules/fastp/main.nf | 2 +- modules/fastp/meta.yml | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/modules/fastp/main.nf b/modules/fastp/main.nf index d8218350..5c9e3b83 100644 --- a/modules/fastp/main.nf +++ b/modules/fastp/main.nf @@ -13,7 +13,7 @@ process FASTP { val save_merged output: - tuple val(meta), path('*.trim.fastq.gz') , emit: reads + tuple val(meta), path('*.trim.fastq.gz') , optional:true, emit: reads tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.log') , emit: log diff --git a/modules/fastp/meta.yml b/modules/fastp/meta.yml index f53bb09f..3274e41b 100644 --- a/modules/fastp/meta.yml +++ b/modules/fastp/meta.yml @@ -22,6 +22,12 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` + - save_merged: + type: boolean + description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz` output: - meta: