add mergekmer module

src/main.nf

@@ -4,8 +4,9 @@ nextflow.enable.dsl=2
 Testing pipeline for marseq scRNASeq analysis
 */
 
-include { FASTKMERS } from "./modules/fastkmers"
 include { SPLIT } from "./modules/split"
+include { FASTKMERS } from "./modules/fastkmers"
+include { MERGEKMER } from "./modules/mergekmer"
 
 
 Channel.fromPath( file(params.csv) )
@@ -21,4 +22,5 @@ Channel.fromPath( file(params.csv) )
 workflow {
   SPLIT(fastq.r1.mix(fastq.r2))
   FASTKMERS(SPLIT.out.fastq.transpose())
+  MERGEKMER(FASTKMERS.out.csv.view())
 }

src/modules/fastkmers.nf

-/*
- * normalize bam file
- */
 process FASTKMERS {
     tag "$meta.id"
     label 'big_mem_mono_cpus'

src/modules/mergekmer.nf

+process MERGEKMER {
+    tag "$meta.id"
+    label 'big_mem_mono_cpus'
+    publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+
+    container "lbmc/mergekmer:0.1.0"
+
+    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 ${meta.id}.csv
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mergekmer: \$(echo \$(mergekmer --version 2>&1))
+    END_VERSIONS
+    """
+}