From 456964fb72be5664d2eb7a0ad8417171bbaef8f4 Mon Sep 17 00:00:00 2001
From: Eva Caceres <eva.caceres@scilifelab.se>
Date: Tue, 14 Jan 2025 15:57:38 +0100
Subject: [PATCH] added haplocheck to multiqc

---
 assets/multiqc_config.yml      | 3 +++
 subworkflows/local/call_snv.nf | 2 ++
 workflows/raredisease.nf       | 1 +
 3 files changed, 6 insertions(+)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 9f87335c..53538d6c 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -19,6 +19,7 @@ export_plots: true
 run_modules:
   - fastqc
   - fastp
+  - haplocheck
   - qualimap
   - picard
   - mosdepth
@@ -39,6 +40,8 @@ module_order:
       name: "fastp"
   - mosdepth:
       name: "Mosdepth"
+  - haplocheck:
+      name: "haplocheck"
   - ngsbits:
       name: "ngsbits"
   - peddy:
diff --git a/subworkflows/local/call_snv.nf b/subworkflows/local/call_snv.nf
index 3e541d42..f0658d2a 100644
--- a/subworkflows/local/call_snv.nf
+++ b/subworkflows/local/call_snv.nf
@@ -132,6 +132,7 @@ workflow CALL_SNV {
             )
             ch_mt_vcf   = POSTPROCESS_MT_CALLS.out.vcf
             ch_mt_tabix = POSTPROCESS_MT_CALLS.out.tbi
+            ch_mt_txt = CALL_SNV_MT.out.txt
             ch_versions = ch_versions.mix(CALL_SNV_MT.out.versions)
             ch_versions = ch_versions.mix(CALL_SNV_MT_SHIFT.out.versions)
             ch_versions = ch_versions.mix(POSTPROCESS_MT_CALLS.out.versions)
@@ -146,5 +147,6 @@ workflow CALL_SNV {
         genome_gtabix    = ch_gtabix           // channel: [ val(meta), path(gtbi) ]
         mt_vcf           = ch_mt_vcf           // channel: [ val(meta), path(vcf) ]
         mt_tabix         = ch_mt_tabix         // channel: [ val(meta), path(tbi) ]
+        mt_txt           = ch_mt_txt           // channel: [ val(meta), path(txt) ]
         versions         = ch_versions         // channel: [ path(versions.yml) ]
 }
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index b606e17d..6742a003 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -916,6 +916,7 @@ workflow RAREDISEASE {
     )
 
     ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
+    ch_multiqc_files = ch_multiqc_files.mix(CALL_SNV.out.mt_txt.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(ALIGN.out.fastp_json.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.sex_check.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))