fix collatekmer

src/main.nf

@@ -27,5 +27,5 @@ workflow {
   FASTKMERS(SPLIT.out.fastq.transpose())
   MERGEKMER(FASTKMERS.out.csv.groupTuple(size: 10))
   MERGEKMER2(MERGEKMER.out.csv.groupTuple())
-  COLLATEKMER(MERGEKMER2.out.csv)
+  COLLATEKMER(MERGEKMER2.out.csv.map{it -> it[1]}.collect())
 }

src/modules/mergekmer.nf

@@ -28,12 +28,12 @@ process MERGEKMER {
 process COLLATEKMER {
     tag "$meta.id"
     label 'big_mem_mono_cpus'
-    publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy'
+    publishDir "results/", mode: 'copy'
 
     container "lbmc/mergekmer:0.1.1"
 
     input:
-    tuple val(meta), path(csv)
+    path(csv)
 
     output:
     tuple val(meta), path("*.csv"), emit: csv
@@ -42,7 +42,7 @@ process COLLATEKMER {
     script:
     def args = task.ext.args ?: ''
     """
-    mergekmer --csv ${csv} --output ${meta.id}.csv --collate
+    mergekmer --csv ${csv} --output final.csv --collate
 
 
     cat <<-END_VERSIONS > versions.yml