flexi_splitter: reformat output file to avoid file name conflict

src/nf_modules/flexi_splitter/main.nf

@@ -4,11 +4,26 @@ container_url = "lbmc/flexi_splitter:${version}"
 params.split = ""
 params.split_out = ""
 
-process split {
+
+workflow split {
+  take:
+    reads
+    config
+  main:
+    split_file(reads, config)
+    split_file.out.fastq.view()
+
+    
+
+  emit:
+    fastq = split_file.out.fastq
+}
+
+process split_file {
   // You can get an example of config file here:
   // src/nf_modules/flexi_splitter/marseq_flexi_splitter.yaml
   container = "${container_url}"
-  label "big_mem_multi_cpus"
+  label "big_mem_mono_cpus"
   tag "$file_prefix"
   if (params.split_out != "") {
     publishDir "results/${params.split_out}", mode: 'copy'
@@ -19,7 +34,7 @@ process split {
   tuple val(config_id), path(config)
 
   output:
-  tuple val(file_id), path("*"), emit: fastq
+  tuple val(file_id), path("split/*/*"), emit: fastq
 
   script:
   if (file_id instanceof List){
@@ -31,9 +46,25 @@ process split {
   if (reads.size() == 2)
   """
   flexi_splitter ${params.split} -n 2 -f ${reads[0]},${reads[1]} -o split -c ${config}
+  rm -Rf split/unassigned
+  find split -type "f" | \
+    sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+    awk '{"mv "\$1" "\$2"}'
+  rm -Rf split
+  mkdir -p results/
+  find split -type "f" | \
+    sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+    awk '{"mv "\$1" results/"\$2"}'
+  rm -Rf split
   """
   else
   """
   flexi_splitter ${params.split} -n 1 -f ${reads[0]} -o split -c ${config}
+  rm -Rf split/unassigned
+  mkdir -p results/
+  find split -type "f" | \
+    sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
+    awk '{"mv "\$1" results/"\$2"}'
+  rm -Rf split
   """
 }