From af1d51303786861d2bc91d7271e3f5805250f028 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 30 Jul 2018 16:46:21 +0200
Subject: [PATCH] Bowtie2: add perl dependency and fix single-end example
---
src/docker_modules/Bowtie2/2.3.4.1/Dockerfile | 4 ++--
src/nf_modules/Bowtie2/bowtie2.nf | 2 +-
src/nf_modules/Bowtie2/tests/mapping_single.nf | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile b/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
index f8b1c5c..0f4ac75 100644
--- a/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
+++ b/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile
@@ -4,8 +4,8 @@ MAINTAINER Laurent Modolo
ENV BOWTIE2_VERSION=2.3.4.1
ENV SAMTOOLS_VERSION=1.7
ENV PACKAGES bowtie2=${BOWTIE2_VERSION}* \
- samtools=${SAMTOOLS_VERSION}*
-
+ samtools=${SAMTOOLS_VERSION}* \
+ perl=5.26.1*
RUN apt-get update && \
apt-get install -y --no-install-recommends ${PACKAGES} && \
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index 9b4203b..18c1479 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -127,7 +127,7 @@ process mapping_fastq {
}
}
"""
-bowtie2 --very_sensitive -p ${task.cpus} -x ${index_id} \
+bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-U ${reads} 2> \
${reads.baseName}_bowtie2_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index b96b108..568a68e 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -33,7 +33,7 @@ process mapping_fastq {
}
}
"""
-bowtie2 --very_sensitive -p ${task.cpus} -x ${index_id} \
+bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-U ${reads} 2> \
${reads.baseName}_bowtie2_report.txt | \
samtools view -Sb - > ${reads.baseName}.bam
--
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