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Verified Commit af1d5130 authored by Laurent Modolo's avatar Laurent Modolo
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Bowtie2: add perl dependency and fix single-end example

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......@@ -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} && \
......
......@@ -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
......
......@@ -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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