nf_modules: add bowtie to DSL2

src/nf_modules/bowtie/main.nf

+version = "1.2.2"
+container_url = "lbmc/bowtie:${version}"
+
+process index_fasta {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$fasta.baseName"
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    path fasta
+
+  output:
+    path "*.index*", emit: index
+    path "*_report.txt", emit: report
+
+  script:
+"""
+bowtie-build --threads ${task.cpus} \
+  -f ${fasta} ${fasta.baseName}.index &> \
+  ${fasta.baseName}_bowtie_index_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie_index_report.txt; then
+  exit 1
+fi
+"""
+}
+
+
+process mapping_fastq_pairedend {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$pair_id"
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  path index
+  tuple val(pair_id), path(reads)
+
+  output:
+  tuple val(pair_id), path("*.bam"), emit: bam
+  path "*_report.txt", emit: report
+
+  script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
+"""
+# -v specify the max number of missmatch, -k the number of match reported per
+# reads
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+  -1 ${reads[0]} -2 ${reads[1]} 2> \
+  ${pair_id}_bowtie_report_tmp.txt | \
+  samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${pair_id}_bowtie_report_tmp.txt > \
+  ${pair_id}_bowtie_mapping_report.txt
+"""
+}
+
+
+process mapping_fastq_singleend {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  publishDir "results/mapping/bams/", mode: 'copy'
+
+  input:
+  path index
+  tuple val(file_id), path(reads)
+
+  output:
+  set file_id, "*.bam", emit: bam
+  file "*_report.txt", emit: report
+
+  script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
+"""
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+  -q ${reads} 2> \
+  ${file_id}_bowtie_report_tmp.txt | \
+  samtools view -Sb - > ${file_id}.bam
+
+if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
+  ${file_id}_bowtie_mapping_report.txt
+"""
+}