add collatekmer step

src/main.nf

@@ -7,6 +7,7 @@ Testing pipeline for marseq scRNASeq analysis
 include { SPLIT } from "./modules/split"
 include { FASTKMERS } from "./modules/fastkmers"
 include { MERGEKMER } from "./modules/mergekmer"
+include { COLLATEKMER } from "./modules/mergekmer"
 
 
 Channel.fromPath( file(params.csv) )
@@ -23,4 +24,5 @@ workflow {
   SPLIT(fastq.r1.mix(fastq.r2))
   FASTKMERS(SPLIT.out.fastq.transpose())
   MERGEKMER(FASTKMERS.out.csv.groupTuple())
+  COLLATEKMER(MERGEKMER.out.csv)
 }

src/modules/mergekmer.nf

@@ -3,7 +3,7 @@ process MERGEKMER {
     label 'big_mem_mono_cpus'
     publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
 
-    container "lbmc/mergekmer:0.1.0"
+    container "lbmc/mergekmer:0.1.1"
 
     input:
     tuple val(meta), path(csv)
@@ -15,7 +15,34 @@ process MERGEKMER {
     script:
     def args = task.ext.args ?: ''
     """
-    mergekmer --csv ${csv} -output ${meta.id}.csv
+    mergekmer --csv ${csv} --output ${meta.id}.csv
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mergekmer: \$(echo \$(mergekmer --version 2>&1))
+    END_VERSIONS
+    """
+}
+
+process COLLATEKMER {
+    tag "$meta.id"
+    label 'big_mem_mono_cpus'
+    publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+
+    container "lbmc/mergekmer:0.1.1"
+
+    input:
+    tuple val(meta), path(csv)
+
+    output:
+    tuple val(meta), path("*.csv"), emit: csv
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mergekmer --csv ${csv} --output ${meta.id}.csv --collate
 
 
     cat <<-END_VERSIONS > versions.yml