From 674c31a51327f5343b8dd21659f3336b25c48481 Mon Sep 17 00:00:00 2001
From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Date: Thu, 27 Jul 2023 11:06:25 +0100
Subject: [PATCH] Fix invalid GATK container (#3673)

Fix GATK container which was invalid

Fixes #3668
---
 modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf | 2 +-
 modules/nf-core/gatk4/germlinecnvcaller/main.nf             | 2 +-
 modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf
index 593c8968e2f..407cc34c982 100644
--- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf
+++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf
@@ -4,7 +4,7 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY {
     label 'process_single'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf
index 9b31c56d386..b5a873aca78 100644
--- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf
+++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf
@@ -3,7 +3,7 @@ process GATK4_GERMLINECNVCALLER {
     label 'process_single'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf
index 8faf0121de9..d1a03fc12c8 100644
--- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf
+++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/main.nf
@@ -3,7 +3,7 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS {
     label 'process_single'
 
     //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
-    container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
+    container "nf-core/gatk:4.4.0.0" //Biocontainers is missing a package
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {