[DSL2] add merge_stats

Author: nservant

conf/modules.config

@@ -100,7 +100,22 @@ process {
 
   withName: 'MERGE_VALID_INTERACTION' {
     publishDir = [
-      path: { "${params.outdir}/hicpro/valid_pairs" },
+      [
+        path: { "${params.outdir}/hicpro/stats/" },
+        mode: 'copy',
+	pattern: "*stat"
+      ],
+      [
+        path: { "${params.outdir}/hicpro/valid_pairs" },
+        mode: 'copy',
+	pattern: "*Pairs"
+      ]
+    ]
+  }
+
+  withName: 'MERGE_STATS' {
+    publishDir = [
+      path: { "${params.outdir}/hicpro/stats" },
       mode: 'copy'
     ]
   }

modules/local/balance.nf~

@@ -0,0 +1,20 @@
+process MERGE_STATS {
+  label 'process_low'
+
+  input:
+  tuple val(meta), path(fstat) 
+
+  output:
+  path("stats/"), emit:mqc_mstats
+  path("*stat"), emit:all_mstats
+
+  script:
+  if ( (fstat =~ /.mapstat/) ){ ext = "mmapstat" }
+  if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
+  if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
+  """
+  merge_statfiles.py -f ${fstat} > ${meta.id}.${ext}
+  mkdir -p stats/${meta.id}
+  cp ${meta.id}.${ext} stats/${meta.id}/
+  """
+}

modules/local/dnase_mapping_stats.nf …ules/local/hicpro/dnase_mapping_stats.nfmodules/local/dnase_mapping_stats.nf renamed to modules/local/hicpro/dnase_mapping_stats.nf modules/local/dnase_mapping_stats.nf renamed to modules/local/hicpro/dnase_mapping_stats.nf

@@ -8,7 +8,7 @@ process MERGE_VALID_INTERACTION {
    output:
    tuple val(meta), path("*.allValidPairs"), emit: valid_pairs
    path("stats/"), emit:mqc
-   path("*mergestat"), emit:stats
+   tuple val(meta), path("*mergestat"), emit:stats
 
    script:
    prefix = meta.id