Merge branch 'master' of gitlab_lbmc:pipelines/nextflow

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

src/nf_modules/FastQC/fastqc.nf

@@ -29,7 +29,7 @@ process fastqc_fastq {
     file reads from fastq_files
 
   output:
-    file "*.{zip,html}" into fastqc_repport
+    file "*.{zip,html}" into fastqc_report
 
   script:
 """
@@ -59,7 +59,7 @@ process fastqc_fastq {
   set pair_id, file(reads) from fastq_files
 
   output:
-    file "*.{zip,html}" into fastqc_repport
+    file "*.{zip,html}" into fastqc_report
 
   script:
 """

src/nf_modules/FastQC/tests/fastqc_paired.nf

@@ -15,7 +15,7 @@ process fastqc_fastq {
   set pair_id, file(reads) from fastq_files
 
   output:
-    file "*.{zip,html}" into fastqc_repport
+    file "*.{zip,html}" into fastqc_report
 
   script:
 """

src/nf_modules/FastQC/tests/fastqc_single.nf

@@ -16,7 +16,7 @@ process fastqc_fastq {
     file reads from fastq_files
 
   output:
-    file "*.{zip,html}" into fastqc_repport
+    file "*.{zip,html}" into fastqc_report
 
   script:
 """

src/nf_modules/MultiQC/multiqc.nf

@@ -7,12 +7,12 @@
 /*                      MultiQC                                     */
 
 process multiqc {
-  tag "$repport.baseName"
+  tag "$report.baseName"
   publishDir "results/fastq/multiqc/", mode: 'copy'
   cpus = 1
 
   input:
-    file repport from fastqc_repport.collect()
+    file report from fastqc_report.collect()
 
   output:
     file "*multiqc_*" into multiqc_report

src/nf_modules/MultiQC/tests/multiqc_paired.nf

@@ -15,7 +15,7 @@ process fastqc_fastq {
   set pair_id, file(reads) from fastq_files
 
   output:
-    file "*.{zip,html}" into fastqc_repport
+    file "*.{zip,html}" into fastqc_report
 
   script:
 """
@@ -25,12 +25,12 @@ ${reads[0]} ${reads[1]}
 }
 
 process multiqc {
-  tag "$repport[0].baseName"
+  tag "$report[0].baseName"
   publishDir "results/fastq/multiqc/", mode: 'copy'
   cpus = 1
 
   input:
-    file repport from fastqc_repport.collect()
+    file report from fastqc_report.collect()
 
   output:
     file "*multiqc_*" into multiqc_report

src/nf_modules/MultiQC/tests/multiqc_single.nf

@@ -16,7 +16,7 @@ process fastqc_fastq {
     file reads from fastq_files
 
   output:
-    file "*.{zip,html}" into fastqc_repport
+    file "*.{zip,html}" into fastqc_report
 
   script:
 """
@@ -25,12 +25,12 @@ fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
 }
 
 process multiqc {
-  tag "$repport[0].baseName"
+  tag "$report[0].baseName"
   publishDir "results/fastq/multiqc/", mode: 'copy'
   cpus = 1
 
   input:
-    file repport from fastqc_repport.collect()
+    file report from fastqc_report.collect()
 
   output:
     file "*multiqc_*" into multiqc_report