UrQt: nf add file_id var for single-end like for paired-end

src/nf_modules/UrQt/tests/trimming_single.nf

@@ -5,24 +5,25 @@ log.info "fastq files : ${params.fastq}"
 Channel
   .fromPath( params.fastq )
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
   .set { fastq_files }
 
 process trimming {
-  tag "$reads.baseName"
+  tag "$file_id"
   cpus 4
 
   input:
-  file reads from fastq_files
+  set file_id, file(reads) from fastq_files
 
   output:
-  file "*_trim.fastq.gz" into fastq_files_trim
+  set file_id, "*_trim.fastq.gz" into fastq_files_trim
 
   script:
   """
   UrQt --t 20 --m ${task.cpus} --gz \
   --in ${reads} \
-  --out ${reads.baseName}_trim.fastq.gz \
-  > ${reads.baseName}_trimming_report.txt
+  --out ${file_id}_trim.fastq.gz \
+  > ${file_id}_trimming_report.txt
   """
 }
 

src/nf_modules/UrQt/urqt.nf

@@ -49,26 +49,24 @@ log.info "fastq files : ${params.fastq}"
 Channel
   .fromPath( params.fastq )
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
   .set { fastq_files }
 
 process trimming {
-  tag "$reads.baseName"
+  tag "$file_id"
   cpus 4
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
-  file reads from fastq_files
+  set file_id, file(reads) from fastq_files
 
   output:
-  file "*_trim.fastq.gz" into fastq_files_trim
+  set file_id, "*_trim.fastq.gz" into fastq_files_trim
 
   script:
-"""
-
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads} \
---out ${reads.baseName}_trim.fastq.gz \
-> ${reads.baseName}_trimming_report.txt
-"""
+  """
+  UrQt --t 20 --m ${task.cpus} --gz \
+  --in ${reads} \
+  --out ${file_id}_trim.fastq.gz \
+  > ${file_id}_trimming_report.txt
+  """
 }
-