From 3064fb6850d85ad100860c5cd07351de65b4cbe8 Mon Sep 17 00:00:00 2001
From: Darryl Nousome <dnousome@gmail.com>
Date: Thu, 2 Jan 2025 14:24:42 -0500
Subject: [PATCH] fix: add process to container

---
 modules/local/deepvariant.nf | 71 +++++++++++++++++++-----------------
 1 file changed, 37 insertions(+), 34 deletions(-)

diff --git a/modules/local/deepvariant.nf b/modules/local/deepvariant.nf
index 9029f84..f05a5f0 100644
--- a/modules/local/deepvariant.nf
+++ b/modules/local/deepvariant.nf
@@ -129,41 +129,8 @@ process bcfconcat {
 }
 
 
-//Combined DeepVariant
-process deepvariant_combined {
-    module = ['deepvariant/1.6.0']
-
-    input:
-        tuple val(samplename), path(bam), path(bai)
-
-    output:
-        tuple val(samplename), path("${samplename}.gvcf.gz"), path("${samplename}.gvcf.gz.tbi"),
-        path("${samplename}.vcf.gz"), path("${samplename}.vcf.gz.tbi")
-
-
-    script:
-    """
-    run_deepvariant \
-        --model_type=WGS \
-        --ref=$GENOMEREF \
-        --reads=${bam} \
-        --output_gvcf=${samplename}.gvcf.gz \
-        --output_vcf=${samplename}.vcf.gz \
-        --num_shards=16
-    """
-
-
-    stub:
-    """
-    touch ${samplename}.vcf.gz ${samplename}.vcf.gz.tbi
-    touch ${samplename}.gvcf.gz  ${samplename}.gvcf.gz.tbi
-    """
-
-
-}
-
 process glnexus {
-    module = ['glnexus/1.4.1','bcftools/1.19']
+    container = "${params.containers.logan}"
 
     input:
         path(gvcfs)
@@ -199,3 +166,39 @@ process glnexus {
         touch germline.norm.vcf.gz.tbi
     """
 }
+
+
+
+
+//Combined DeepVariant
+process deepvariant_combined {
+    module = ['deepvariant/1.6.0']
+
+    input:
+        tuple val(samplename), path(bam), path(bai)
+
+    output:
+        tuple val(samplename), path("${samplename}.gvcf.gz"), path("${samplename}.gvcf.gz.tbi"),
+        path("${samplename}.vcf.gz"), path("${samplename}.vcf.gz.tbi")
+
+
+    script:
+    """
+    run_deepvariant \
+        --model_type=WGS \
+        --ref=$GENOMEREF \
+        --reads=${bam} \
+        --output_gvcf=${samplename}.gvcf.gz \
+        --output_vcf=${samplename}.vcf.gz \
+        --num_shards=16
+    """
+
+
+    stub:
+    """
+    touch ${samplename}.vcf.gz ${samplename}.vcf.gz.tbi
+    touch ${samplename}.gvcf.gz  ${samplename}.gvcf.gz.tbi
+    """
+
+
+}
\ No newline at end of file