bam_mapped have single and multiple bams

main.nf

@@ -367,16 +367,17 @@ workflow {
             single:   it[2].size() == 1
             multiple: it[2].size() > 1
         }.set { bam }
-    bam.single.map {
-        idPatient, idSample, idRun, bam ->
-        [idPatient, idSample, bam]
-    }
 
-    bam.single.view()
-    bam.multiple.view()
+    bam_single = bam.single.map {
+        idPatient, idSample, idRun, bam, bai ->
+        [idPatient, idSample, bam[0], bai[0]]
+    }
 
     //multipleBam = multipleBam.mix(multipleBamSentieon)
-    MERGE_BAM_MAPPED(bam.multiple)
+
+    bam_mapped = bam_single.mix(MERGE_BAM_MAPPED(bam.multiple))
+
+    bam_mapped.view()
 
     OUTPUT_DOCUMENTATION(
         output_docs,

modules/local/merge_mapped_bam.nf

@@ -1,16 +1,17 @@
 process MERGE_BAM_MAPPED {
     label 'cpus'
 
-    tag "${idPatient}-${idSample}"
+    tag "${patient}-${sample}"
 
     input:
-        tuple idPatient, idSample, idRun, path(bam), path(bai)// from multiple
+        tuple patient, sample, run, path(bam), path(bai)
 
     output:
-        tuple idPatient, idSample, path("${idSample}.bam") //into bam_mapped_merged
+        tuple patient, sample, path("${sample}.bam"), path("${sample}.bam.bai")
 
     script:
     """
-    samtools merge --threads ${task.cpus} ${idSample}.bam ${bam}
+    samtools merge --threads ${task.cpus} ${sample}.bam ${bam}
+    samtools index ${sample}.bam
     """
 }