diff --git a/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile b/src/docker_modules/Bowtie2/2.3.4.1/Dockerfile index f8b1c5c048257ada6d0892dc787bd943aa2739b5..0f4ac75e48b5390714a22765c93939b72650b47e 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 9b4203b3b7cb733843e06854e6d0b3ca60fb8d7e..18c1479be848a7ebef5ef1de709d6de19f23fe4e 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 b96b108c4cf9fcc8574247a4a25470cb5b11f49e..568a68ea1983a13336da7653113a0de047bc2859 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