From 5d72500d601432f5396e9022c3a709854197db1a Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Sun, 22 May 2022 13:34:56 +0200
Subject: [PATCH] remove variables used for test data generation, add tbi

---
 modules/gatk4/cnnscorevariants/main.nf       | 9 +++++----
 modules/gatk4/cnnscorevariants/meta.yml      | 8 ++++++++
 modules/gatk4/filtervarianttranches/main.nf  | 7 ++++---
 modules/gatk4/filtervarianttranches/meta.yml | 4 ++++
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/modules/gatk4/cnnscorevariants/main.nf b/modules/gatk4/cnnscorevariants/main.nf
index c02c6035..a1bb3811 100644
--- a/modules/gatk4/cnnscorevariants/main.nf
+++ b/modules/gatk4/cnnscorevariants/main.nf
@@ -9,7 +9,7 @@ process GATK4_CNNSCOREVARIANTS {
     container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
 
     input:
-    tuple val(meta), path(vcf), path(aligned_input), path(intervals)
+    tuple val(meta), path(vcf), path(tbi), path(aligned_input), path(intervals)
     path fasta
     path fai
     path dict
@@ -17,8 +17,9 @@ process GATK4_CNNSCOREVARIANTS {
     path weights
 
     output:
-    tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*cnn.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*cnn.vcf.gz.tbi"), emit: tbi
+    path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -40,7 +41,7 @@ process GATK4_CNNSCOREVARIANTS {
     """
     gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
         --variant $vcf \\
-        --output ${prefix}.vcf.gz \\
+        --output ${prefix}.cnn.vcf.gz \\
         --reference $fasta \\
         $interval_command \\
         $aligned_input \\
diff --git a/modules/gatk4/cnnscorevariants/meta.yml b/modules/gatk4/cnnscorevariants/meta.yml
index 1d47e6e7..4e59cb8e 100644
--- a/modules/gatk4/cnnscorevariants/meta.yml
+++ b/modules/gatk4/cnnscorevariants/meta.yml
@@ -25,6 +25,10 @@ input:
       type: file
       description: VCF file
       pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: VCF index file
+      pattern: "*.vcf.gz.tbi"
   - aligned_input:
       type: file
       description: BAM/CRAM file from alignment (optional)
@@ -67,6 +71,10 @@ output:
       type: file
       description: Annotated VCF file
       pattern: "*.vcf"
+  - tbi:
+      type: file
+      description: VCF index file
+      pattern: "*.vcf.gz.tbi"
 
 authors:
   - "@FriederikeHanssen"
diff --git a/modules/gatk4/filtervarianttranches/main.nf b/modules/gatk4/filtervarianttranches/main.nf
index 2887324b..03323744 100644
--- a/modules/gatk4/filtervarianttranches/main.nf
+++ b/modules/gatk4/filtervarianttranches/main.nf
@@ -8,7 +8,7 @@ process GATK4_FILTERVARIANTTRANCHES {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi),path(intervals)
+    tuple val(meta), path(vcf), path(tbi), path(intervals)
     path resources
     path resources_index
     path fasta
@@ -17,8 +17,9 @@ process GATK4_FILTERVARIANTTRANCHES {
 
 
     output:
-    tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "versions.yml"              , emit: versions
+    tuple val(meta), path("*.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/gatk4/filtervarianttranches/meta.yml b/modules/gatk4/filtervarianttranches/meta.yml
index 7682b534..f89063a5 100644
--- a/modules/gatk4/filtervarianttranches/meta.yml
+++ b/modules/gatk4/filtervarianttranches/meta.yml
@@ -59,6 +59,10 @@ output:
       type: file
       description: VCF file
       pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: VCF index file
+      pattern: "*.vcf.gz.tbi"
 
 authors:
   - "@FriederikeHanssen"