From 0ed87085a90b711f8a886cf4932d1cc05a4e741d Mon Sep 17 00:00:00 2001
From: atrigila <18577080+atrigila@users.noreply.github.com>
Date: Sat, 20 Apr 2024 12:23:47 +0000
Subject: [PATCH] index concat files

---
 conf/quilt_subworkflow.config                       | 13 +++++++++++++
 .../vcf_concatenate_bcftools.nf                     |  9 ++++++++-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/conf/quilt_subworkflow.config b/conf/quilt_subworkflow.config
index ef309039..6f237032 100644
--- a/conf/quilt_subworkflow.config
+++ b/conf/quilt_subworkflow.config
@@ -119,4 +119,17 @@ process {
         ]
     }
 
+        withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCATENATE_BCFTOOLS:BCFTOOLS_INDEX' {
+        ext.args     = {[
+                        "--tbi",
+                        ].join(" ").trim()}
+
+        publishDir = [
+            [
+                path: { "${params.outdir}/quilt_impute/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}/concat" },
+                mode: params.publish_dir_mode,
+            ],
+        ]
+    }
+
 }
diff --git a/subworkflows/local/vcf_concatenate_bcftools/vcf_concatenate_bcftools.nf b/subworkflows/local/vcf_concatenate_bcftools/vcf_concatenate_bcftools.nf
index fd02a40b..6653d765 100644
--- a/subworkflows/local/vcf_concatenate_bcftools/vcf_concatenate_bcftools.nf
+++ b/subworkflows/local/vcf_concatenate_bcftools/vcf_concatenate_bcftools.nf
@@ -1,4 +1,5 @@
 include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main'
+include { BCFTOOLS_INDEX  } from '../../../modules/nf-core/bcftools/index/main'
 
 workflow VCF_CONCATENATE_BCFTOOLS {
 
@@ -17,7 +18,13 @@ workflow VCF_CONCATENATE_BCFTOOLS {
     // Ligate and concatenate chunks
     BCFTOOLS_CONCAT(ch_vcf_tbi_grouped)
 
+    // Index concatenated VCF
+    BCFTOOLS_INDEX(BCFTOOLS_CONCAT.out.vcf)
+
+    // Join VCFs and TBIs
+    ch_imputed_vcf_tbi = BCFTOOLS_CONCAT.out.vcf.join(BCFTOOLS_INDEX.out.tbi)
+
     emit:
-    ch_concat_vcf =  BCFTOOLS_CONCAT.out.vcf
+    ch_imputed_vcf_tbi                          // channel:  [ meta, vcf, tbi ]
 
     }