From 884afee051444e7d9f32c67c671f70e7d4209ef5 Mon Sep 17 00:00:00 2001
From: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch>
Date: Wed, 18 Mar 2020 08:59:49 +0100
Subject: [PATCH] Fix cutadapt log file names
---
workflow/rules/paired_end.snakefile.smk | 6 +++---
workflow/rules/single_end.snakefile.smk | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index d49d55f..f7326c3 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -24,7 +24,7 @@ rule pe_fastqc:
threads: 2
singularity:
- "docker://zavolab/fastqc:0.11.9"
+ "docker://zavolab/fastqc:0.11.9-slim"
log:
stderr = os.path.join(
@@ -109,7 +109,7 @@ rule pe_remove_adapters_cutadapt:
-o {output.reads1} \
-p {output.reads2} \
{input.reads1} \
- {input.reads2}); \
+ {input.reads2};) \
1> {log.stdout} 2>{log.stderr}"
@@ -162,7 +162,7 @@ rule pe_remove_polya_cutadapt:
config["log_dir"],
"paired_end",
"{sample}",
- "remove_adapters_cutadapt.stdout.log")
+ "remove_polya_cutadapt.stdout.log")
shell:
"(cutadapt \
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 3857baa..415634d 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -136,7 +136,7 @@ rule remove_polya_cutadapt:
-m 10 \
-a {params.polya_3} \
-o {output.reads} \
- {input.reads}); \
+ {input.reads};) \
1> {log.stdout} 2> {log.stderr}"
--
GitLab