Update groupTuple for merging and fix input sorting for Zerone - reso…

…lves #3

chipseq-pipeline.nf

@@ -231,7 +231,7 @@ process mapping {
 singleBams = Channel.create()
 groupedBams = Channel.create()
 
-bams.groupTuple(by: [0,3,4])
+bams.groupTuple(by: [0,3,4,5,6])
 .choice(singleBams, groupedBams) {
   it[2].size() > 1 ? 1 : 0
 }
@@ -246,7 +246,7 @@ process mergeBam {
 
     script:
     def cpus = task.cpus
-    def prefix = prefix.sort().join(':')
+    prefix = prefix.sort().join(':')
     """
     (
       samtools view -H ${bam} | grep -v '@RG';
@@ -261,6 +261,8 @@ process mergeBam {
     """
 }
 
+mergedBams.println()
+return
 
 singleBams
 .mix(mergedBams)
@@ -391,7 +393,7 @@ controlBams
   sampleId = replicateId.replaceAll(/${params.replicatePattern}$/,'')
   [sampleId, bam, control, mark, view]
 }
-.groupTuple(by:[0,3,4])
+.groupTuple(by:[0,3,4], sort: {it.baseName})
 .set {bamsZerone}
 
 def globalFragmentLength = params.fragmentLength ?: defaults.fragmentLength
@@ -610,9 +612,9 @@ process zerone {
   def awkScaleMergedBed = '$0~/^#/ || $NF=$NF*1000'
   def awkMatrix2Bed = '$0~/^#/ || $0=$1 OFS $2 OFS $3 OFS $NF*1000'
   """
-  zerone -c ${params.zeroneMinConfidence} -0 ${control.sort().join(",")} -1 ${bam.sort().join(",")} > ${prefix}_zerone.01
+  zerone -c ${params.zeroneMinConfidence} -0 ${control.join(",")} -1 ${bam.join(",")} > ${prefix}_zerone.01
   awk -F"\\t" '${awkMatrix2Bed}' OFS="\\t" ${prefix}_zerone.01 > ${prefix}_zerone.bed
-  zerone -c ${params.zeroneMinConfidence} -l -0 ${control.sort().join(",")} -1 ${bam.sort().join(",")} | awk -F"\\t" '${awkScaleMergedBed}' OFS="\\t" > ${prefix}_zerone_merged.bed
+  zerone -c ${params.zeroneMinConfidence} -l -0 ${control.join(",")} -1 ${bam.join(",")} | awk -F"\\t" '${awkScaleMergedBed}' OFS="\\t" > ${prefix}_zerone_merged.bed
   """
 }