Fix routing for PE/SE channels

workflow/main.nf

@@ -21,6 +21,9 @@ index_name = "genome"
 // which is covered by the GNU General Public License v3
 // https://github.com/nextflow-io/rnatoy/blob/master/main.nf
 
+read_pe = Channel.empty()
+read_se = Channel.empty()
+
 if (params.pairs == 'pe') {
 Channel
   .fromPath( fastqs )
@@ -31,20 +34,21 @@ Channel
   }
   .groupTuple(sort: true)
   .map { id, files -> tuple(id, files[0],files[1])}
-  .set { read_pe }
-  }
+  .into { read_pe }
+}
+
 if (params.pairs == 'se') {
 Channel
   .fromPath( fastqs )
   .ifEmpty { error "Cannot find any files matching: ${fastqs}" }
   .map { path ->
-       def prefix = readPrefix(path, '*{1,2}.{fastq,fq}{,.gz}')
+       def prefix = readPrefix(path, '*.{fastq,fq}{,.gz}')
        tuple(prefix, path)
   }
   .groupTuple(sort: true)
   .map { id, files -> tuple(id, files[0])}
-  .set { read_se }
-  }
+  .into { read_se }
+}
 
 /*
  * Helper function, given a file Path
@@ -133,9 +137,8 @@ process alignpe {
   input:
   set pair_id, file(fq1), file(fq2) from trimpe
   output:
-  set pair_id, file("${pair_id}.bam") into aligned
-  set pair_id, file("${pair_id}.bam") into aligned2
-  file("${pair_id}.flagstat.txt") into alignstats
+  set pair_id, file("${pair_id}.bam") into aligned_pe
+  file("${pair_id}.flagstat.txt") into alignstats_pe
   """
   module load hisat2/2.0.1-beta-intel samtools/intel/1.3 fastqc/0.11.2 picard/1.127
   hisat2 -p 4 --no-unal --dta -x ${index_path}/${index_name} -1 ${fq1} -2 ${fq2} -S out.sam 2> ${pair_id}.hisatout.txt
@@ -155,9 +158,8 @@ process alignse {
   input:
   set pair_id, file(fq1) from trimse
   output:
-  set pair_id, file("${pair_id}.bam") into aligned
-  set pair_id, file("${pair_id}.bam") into aligned2
-  file("${pair_id}.flagstat.txt") into alignstats
+  set pair_id, file("${pair_id}.bam") into aligned_se
+  file("${pair_id}.flagstat.txt") into alignstats_se
   """
   module load hisat2/2.0.1-beta-intel samtools/intel/1.3 fastqc/0.11.2 picard/1.127
   hisat2 -p 4 --no-unal --dta -x ${index_path}/${index_name} -U ${fq1} -S out.sam 2> ${pair_id}.hisatout.txt
@@ -170,6 +172,20 @@ process alignse {
   """
 }
 
+// From here on we are the same for PE and SE, so merge channels and carry on
+
+Channel
+  .empty()
+  .mix(aligned_se, aligned_pe)
+  .tap { aligned2 }
+  .set { aligned }
+
+Channel
+  .empty()
+  .mix(alignstats_se, alignstats_pe)
+  .set { alignstats }
+
+
 //
 // Summarize all flagstat output
 //