nf_modules: add urqt for DSL2

src/nf_modules/cutadapt/main.nf

@@ -6,7 +6,7 @@ adapter_5_prim = "CTCTTCCGATCT"
 trim_quality = "20"
 
 
-process adaptor_removal_paired {
+process adaptor_removal_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"

src/nf_modules/urqt/main.nf

+version = "d62c1f8"
+container_url = "lbmc/urqt:${version}"
+
+trim_quality = "20"
+
+process trimming_pairedend {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "${reads}"
+  publishDir "results/fastq/trimming/", mode: 'copy'
+
+  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:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+  --in ${reads[0]} --inpair ${reads[1]} \
+  --out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+  > ${pair_id}_trimming_report.txt
+"""
+}
+
+process trimming_singleend {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "$file_id"
+  publishDir "results/fastq/trimming/", mode: 'copy'
+
+  input:
+  tuple val(file_id), path(reads)
+
+  output:
+  tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq
+  path "*_report.txt", emit: report
+
+  script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+  --in ${reads} \
+  --out ${file_id}_trim.fastq.gz \
+  > ${file_id}_trimming_report.txt
+"""
+}
+