From c46f434f28942ced9fa2eb5d94b5745d076057b4 Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Wed, 10 Nov 2021 16:42:04 +0100
Subject: [PATCH] fix error with PE when checking of extension in STAR rules
---
workflow/rules/star_mapping_pass1.rules | 5 ++++-
workflow/rules/star_mapping_pass2.rules | 5 ++++-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/workflow/rules/star_mapping_pass1.rules b/workflow/rules/star_mapping_pass1.rules
index 516ead4..3929b94 100755
--- a/workflow/rules/star_mapping_pass1.rules
+++ b/workflow/rules/star_mapping_pass1.rules
@@ -45,7 +45,10 @@ rule star_mapping_pass1:
star_mapping_pass1_logs
shell:
"""
- if [[ {input.fastq} == "*.gz" ]]
+ tmp="{input}"
+ infiles=($tmp)
+
+ if [[ ${{infiles[0]}} == "*.gz" ]]
then
STAR --genomeDir {params.index} \
--readFilesIn {input.fastq} \
diff --git a/workflow/rules/star_mapping_pass2.rules b/workflow/rules/star_mapping_pass2.rules
index daae75f..86bf57f 100755
--- a/workflow/rules/star_mapping_pass2.rules
+++ b/workflow/rules/star_mapping_pass2.rules
@@ -46,7 +46,10 @@ rule star_mapping_pass2:
star_mapping_pass2_logs
shell:
"""
- if [[ {input.fastq} == "*.gz" ]]
+ tmp="{input}"
+ infiles=($tmp)
+
+ if [[ ${{infiles[0]}} == "*.gz" ]]
then
STAR --genomeDir {params.index} \
--readFilesIn {input.fastq} \
--
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