From 0b47a08389b18984f051be813f96971ebec9d941 Mon Sep 17 00:00:00 2001 From: magodfroid Date: Thu, 26 Oct 2023 16:40:12 +0200 Subject: [PATCH] [mg] hotfix - reverted to pipe and trim_tail was incorrectly set --- workflow/Snakefile | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index ad3616ea..e688f32a 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -76,7 +76,7 @@ rule all: if common_config["platform"] =="TempO-Seq": length_required_fastp = 50 - trim_tail1_fastp = 0 + trim_tail1_fastp = 1 else: length_required_fastp = 36 trim_tail1_fastp = 0 @@ -85,7 +85,7 @@ rule fastp_se: input: R1 = ancient(str(raw_dir / "{sample}.fastq.gz")) output: - R1 = temp(trim_dir / "{sample}.fastq.gz"), + R1 = pipe(trim_dir / "{sample}.fastq.gz"), json = trim_dir / "{sample}_fastp.json", html = trim_dir / "{sample}_fastp.html" conda: @@ -129,8 +129,8 @@ rule fastp_pe: R1 = ancient(str(raw_dir / "{sample}.R1.fastq.gz")), R2 = ancient(str(raw_dir / "{sample}.R2.fastq.gz")) output: - R1 = temp(trim_dir / "{sample}.R1.fastq.gz"), - R2 = temp(trim_dir / "{sample}.R2.fastq.gz"), + R1 = pipe(trim_dir / "{sample}.R1.fastq.gz"), + R2 = pipe(trim_dir / "{sample}.R2.fastq.gz"), json = trim_dir / "{sample}_fastp.json", html = trim_dir / "{sample}_fastp.html" conda: