Bowtie2: add perl dependency and fix single-end example

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} && \

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

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