add paired_end and single_end switch version to all implementations

src/nf_modules/bowtie/main.nf

@@ -25,6 +25,55 @@ fi
 """
 }
 
+process mapping_fastq {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$pair_id"
+
+  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]
+    }
+  }
+if (reads instanceof List)
+"""
+# -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
+"""
+else
+"""
+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
+"""
+}
 
 process mapping_fastq_pairedend {
   container = "${container_url}"

src/nf_modules/bowtie2/main.nf

@@ -27,6 +27,59 @@ fi
 }
 
 
+process mapping_fastq {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$pair_id"
+
+  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]
+    }
+  }
+if (reads instanceof List)
+"""
+bowtie2 --very-sensitive \
+  -p ${task.cpus} \
+  -x ${index_id} \
+  -1 ${reads[0]} \
+  -2 ${reads[1]} 2> \
+  ${pair_id}_bowtie2_mapping_report_tmp.txt | \
+  samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie2_mapping_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${pair_id}_bowtie2_mapping_report_tmp.txt > \
+  ${pair_id}_bowtie2_mapping_report.txt
+"""
+else
+"""
+bowtie2 --very-sensitive \
+  -p ${task.cpus} \
+  -x ${index_id} \
+  -U ${reads} 2> \
+  ${reads.baseName}_bowtie2_mapping_report_tmp.txt | \
+  samtools view -Sb - > ${reads.baseName}.bam
+
+if grep -q "Error" ${reads.baseName}_bowtie2_mapping_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${reads.baseName}_bowtie2_mapping_report_tmp.txt > \
+  ${reads.baseName}_bowtie2_mapping_report.txt
+"""
+}
+
 process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"

src/nf_modules/cutadapt/main.nf

@@ -6,6 +6,33 @@ adapter_5_prim = "CTCTTCCGATCT"
 trim_quality = "20"
 
 
+process adaptor_removal {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$pair_id"
+
+  input:
+  tuple val(pair_id), path(reads)
+
+  output:
+  tuple val(pair_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq
+  path "*_report.txt", emit: report
+
+  script:
+if (reads instanceof List)
+  """
+  cutadapt -a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim} \
+  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+else:
+  """
+  cutadapt -a ${adapter_3_prim} -g ${adapter_5_prim} \
+  -o ${file_id}_cut.fastq.gz \
+  ${reads} > ${file_id}_report.txt
+  """
+}
+
 process adaptor_removal_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
@@ -46,6 +73,33 @@ process adaptor_removal_singleend {
   """
 }
 
+process trimming_pairedend {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "$pair_id"
+
+  input:
+  tuple val(pair_id), path(reads)
+
+  output:
+  tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
+  path "*_report.txt", emit: report
+
+  script:
+if (reads instanceof List)
+  """
+  cutadapt -q ${trim_quality},${trim_quality} \
+  -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+else
+  """
+  cutadapt -q ${trim_quality},${trim_quality} \
+  -o ${file_id}_trim.fastq.gz \
+  ${reads} > ${file_id}_report.txt
+  """
+}
+
 process trimming_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"