pg-main from prod server added

pgx-main/tests/simulations/gen_dips.nf

@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+//haps1 = Channel.fromFilePairs(params.in_pgvcf, type: 'file') { file -> file.name.replaceAll(/.vcf.gz|.tbi$/,'') }
+
+haps1 = Channel.fromPath(params.in_hap1, type: 'file')
+haps2 = Channel.fromPath(params.in_hap2, type: 'file') 
+
+//haps2 = Channel.fromFilePairs(params.in_haplo, type: 'file') { file -> file.name.replaceAll(/.vcf.gz|.tbi$/,'') }
+
+haps1
+    .combine(haps2)
+    .set {data}
+//    .println()
+
+
+process make_diplo {
+//   maxForks 10
+//   errorStrategy 'ignore'
+//   tag "${name}" 
+//   label 'big_mem'
+   publishDir params.out_dir, mode: 'copy', overwrite: 'true'
+
+   input:
+      file(vcfs) from data   
+
+   output:	        
+      file("*_diplo.vcf.gz") into diplotypes_ch
+     
+   script:
+    """ 
+    tabix ${vcfs.get(0)}
+    tabix ${vcfs.get(1)}
+    bcftools merge ${vcfs.get(0)} ${vcfs.get(1)} | bgzip -c > ${vcfs.get(0).name.replace(/.vcf.gz/, "")}_${vcfs.get(1).name.replace(/.vcf.gz/, "")}_diplo.vcf.gz
+    """
+
+}