Add merge_bams process

main.nf

@@ -253,10 +253,12 @@ if (params.sentieon) log.warn "[nf-core/sarek] Sentieon will be used, only works
 ================================================================================
 */
 
+
 include { BWAMEM2_MEM }           from './modules/local/bwamem2_mem.nf'
 include { GET_SOFTWARE_VERSIONS } from './modules/local/get_software_versions'
 include { OUTPUT_DOCUMENTATION }  from './modules/local/output_documentation'
 include { TRIM_GALORE }           from './modules/local/trim_galore.nf'
+include { MERGE_BAM_MAPPED }      from './modules/local/merge_mapped_bam' addParams(params)
 
 /*
 ================================================================================
@@ -360,6 +362,22 @@ workflow {
         BWAMEM2_MEM(input_sample, bwa, fasta, fai)
     }
 
+    BWAMEM2_MEM.out.groupTuple(by:[0, 1])
+        .branch {
+            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()
+
+    //multipleBam = multipleBam.mix(multipleBamSentieon)
+    MERGE_BAM_MAPPED(bam.multiple)
+
     OUTPUT_DOCUMENTATION(
         output_docs,
         output_docs_images)

modules/local/merge_mapped_bam.nf

@@ -0,0 +1,16 @@
+process MERGE_BAM_MAPPED {
+    label 'cpus'
+
+    tag "${idPatient}-${idSample}"
+
+    input:
+        tuple idPatient, idSample, idRun, path(bam), path(bai)// from multiple
+
+    output:
+        tuple idPatient, idSample, path("${idSample}.bam") //into bam_mapped_merged
+
+    script:
+    """
+    samtools merge --threads ${task.cpus} ${idSample}.bam ${bam}
+    """
+}