Bowtie2: fix bug on nf files

src/nf_modules/Bowtie2/bowtie2.nf

@@ -57,16 +57,17 @@ Channel
   .set { index_files }
 
 process mapping_fastq {
-  tag "$reads.baseName"
+  tag "$pair_id"
   cpus 4
   publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
-  file reads from fastq_files
+  set pair_id, file(reads) from fastq_files
   file index from index_files.toList()
 
   output:
-  file "*.bam" into bam_files
+  set pair_id, "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]
@@ -76,12 +77,12 @@ process mapping_fastq {
     }
   }
 """
-bowtie2 --very_sensitive -p ${task.cpus} -x ${index_id} \
--U ${reads} 2> \
-${reads.baseName}_bowtie2_report.txt | \
-samtools view -Sb - > ${reads.baseName}.bam
+bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
+-1 ${reads[0]} -2 ${reads[1]} 2> \
+${pair_id}_bowtie2_report.txt | \
+samtools view -Sb - > ${pair_id}.bam
 
-if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
   exit 1
 fi
 """
@@ -116,15 +117,22 @@ 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\.bt2/) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
 """
-bowtie2 --very_sensitive -p ${task.cpus} -x ${index[0].baseName} \
+bowtie2 --very_sensitive -p ${task.cpus} -x ${index_id} \
 -U ${reads} 2> \
 ${reads.baseName}_bowtie2_report.txt | \
 samtools view -Sb - > ${reads.baseName}.bam
 
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${reads.baseName}_bowtie2_report.txt; then
   exit 1
 fi
 """

src/nf_modules/Bowtie2/tests/mapping_paired.nf

@@ -24,6 +24,7 @@ process mapping_fastq {
 
   output:
   set pair_id, "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]

src/nf_modules/Bowtie2/tests/mapping_single.nf

@@ -23,6 +23,7 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]