Merge branch 'master' of gitlab_lbmc:pipelines/nextflow

README.md

@@ -5,7 +5,7 @@ You can fork this repository to build your own pipeline.
 To get the last commits from this repository into your fork use the following commands:
 
 ```sh
-git remote add upstream https://gitlab.biologie.ens-lyon.fr/pipelines/nextflow.git
+git remote add upstream gitlab_lbmc:pipelines/nextflow.git
 git pull upstream master
 ```
 

src/nf_modules/Bowtie/bowtie.nf

@@ -25,6 +25,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """
@@ -68,6 +69,7 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]
@@ -119,6 +121,7 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
 index_id = index[0]

src/nf_modules/Bowtie/tests/index.nf

@@ -17,6 +17,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """

src/nf_modules/Bowtie/tests/mapping_paired.nf

@@ -24,11 +24,12 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.ebwt/) {
+  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
         index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
     }
   }

src/nf_modules/Bowtie/tests/mapping_single.nf

@@ -23,17 +23,18 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
 index_id = index[0]
 for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/) {
+  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
       index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
   }
 }
 """
 bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--U ${reads} 2> \
+-q ${reads} 2> \
 ${reads.baseName}_bowtie_report.txt | \
 samtools view -Sb - > ${reads.baseName}.bam
 

src/nf_modules/Bowtie2/bowtie2.nf

@@ -25,6 +25,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """
@@ -72,7 +73,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }
@@ -122,7 +123,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }

src/nf_modules/Bowtie2/tests/index.nf

@@ -17,6 +17,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """

src/nf_modules/Bowtie2/tests/mapping_paired.nf

@@ -29,7 +29,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }

src/nf_modules/Bowtie2/tests/mapping_single.nf

@@ -28,7 +28,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }