From 698e9979b5939d2c8f25e3a1e2b526c56336792d Mon Sep 17 00:00:00 2001 From: Adam Talbot Date: Thu, 27 Jul 2023 10:46:20 +0100 Subject: [PATCH] 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) {