kallisto: update script to match CONTRIBUTING.md

src/nf_modules/kallisto/main.nf

@@ -45,79 +45,23 @@ process mapping_fastq {
 
   script:
   if (file_id instanceof List){
-    pair_id = file_id[0]
+    file_prefix = file_id[0]
   } else {
-    pair_id = file_id
+    file_prefix = file_id
   }
 
-  if (reads instanceof List)
+  if (reads.size() == 2)
   """
-  mkdir ${pair_id}
+  mkdir ${file_prefix}
   kallisto quant -i ${index} -t ${task.cpus} \
-  ${params.mapping_fastq} -o ${pair_id} \
-  ${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
+  ${params.mapping_fastq} -o ${file_prefix} \
+  ${reads[0]} ${reads[1]} &> ${file_prefix}_kallisto_mapping_report.txt
   """
-  else
+  else if (reads.size() == 1)
   """
-  mkdir ${pair_id}
+  mkdir ${file_prefix}
   kallisto quant -i ${index} -t ${task.cpus} --single \
-  ${params.mapping_fastq} -o ${pair_id} \
-  ${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
+  ${params.mapping_fastq} -o ${file_prefix} \
+  ${reads} &> ${file_prefix}_kallisto_mapping_report.txt
   """
 }
-
-params.mapping_fastq_pairedend = "--bias --bootstrap-samples 100"
-params.mapping_fastq_pairedend_out = ""
-process mapping_fastq_pairedend {
-  container = "${container_url}"
-  label "big_mem_multi_cpus"
-  tag "$pair_id"
-  if (params.mapping_fastq_pairedend_out != "") {
-    publishDir "results/${params.mapping_fastq_pairedend_out}", mode: 'copy'
-  }
-
-  input:
-  tuple val(index_id), path(index)
-  tuple val(pair_id), path(reads)
-
-  output:
-  tuple val(pair_id), path("${pair_id}"), emit: counts
-  tuple val(pair_id), path("*_report.txt"), emit: report
-
-  script:
-"""
-mkdir ${pair_id}
-kallisto quant -i ${index} -t ${task.cpus} \
-${params.mapping_fastq_pairedend} -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
-"""
-}
-
-
-params.mapping_fastq_singleend = "--bias --bootstrap-samples 100"
-params.mapping_fastq_singleend_out = ""
-process mapping_fastq_singleend {
-  container = "${container_url}"
-  label "big_mem_multi_cpus"
-  tag "$file_id"
-  if (params.mapping_fastq_singleend_out != "") {
-    publishDir "results/${params.mapping_fastq_singleend_out}", mode: 'copy'
-  }
-
-  input:
-  tuple val(index_id), path(index)
-  tuple val(file_id), path(reads)
-
-  output:
-  tuple val(file_id), path("${pair_id}"), emit: counts
-  tuple val(file_id), path("*_report.txt"), emit: report
-
-  script:
-"""
-mkdir ${file_id}
-kallisto quant -i ${index} -t ${task.cpus} --single \
-${params.mapping_fastq_singleend} -o ${file_id} \
--l ${params.mean} -s ${params.sd} \
-${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
-"""
-}