From 74376ab6334071073ada0c0b7eb01764bbbf43c7 Mon Sep 17 00:00:00 2001
From: ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Sun, 9 Jun 2019 23:53:20 +0200
Subject: [PATCH] edit multiqc_raw to force overwritting existing multiqc
reports AND remove line in fastqc_raw that created non-needed directory
---
rules/rawQC.smk | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/rules/rawQC.smk b/rules/rawQC.smk
index 5bb0bcb..0f1997c 100644
--- a/rules/rawQC.smk
+++ b/rules/rawQC.smk
@@ -35,9 +35,6 @@ rule fastqc_raw:
singularity: singularity_img
shell:
'''
- # checks if output dir exist, created otherwise
- [ ! -d {params.fastqc_dir}/{wildcards.dataset} ] && \
- mkdir {params.fastqc_dir}/{wildcards.dataset}
# Take a random sample of reads (1%) and process them with fastQC
(reformat.sh in={input} out=stdout.fq samplerate={params.samplerate} | \
fastqc -o {params.fastqc_dir}/{wildcards.dataset}_fastqc -f fastq \
@@ -72,5 +69,5 @@ rule multiqc_raw:
singularity:singularity_img
shell:
'''
- multiqc --file-list {input} --filename {output.multiqc_report}
+ multiqc -f --file-list {input} --filename {output.multiqc_report}
'''
--
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