From 38d779b1dcd33c53b4e61fe70c30acd0e631308f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 30 Sep 2023 16:01:09 -0500
Subject: [PATCH] fix: Use GitHub containers registry for HapLink modules

There are still issues with using the Biocontainers build of HapLink within
certain container platforms (cough, Singularity). Use the more exotic, but
more stable, one directly from the lab.
---
 modules/haplink/haplotypes/main.nf | 2 +-
 modules/haplink/sequences/main.nf  | 2 +-
 modules/haplink/variants/main.nf   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/haplink/haplotypes/main.nf b/modules/haplink/haplotypes/main.nf
index 5673af4..dc84ef8 100644
--- a/modules/haplink/haplotypes/main.nf
+++ b/modules/haplink/haplotypes/main.nf
@@ -3,7 +3,7 @@ process HAPLINK_HAPLOTYPES {
     label 'process_high'
     label 'haplink'
 
-    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+    container 'ghcr.io/ksumngs/haplink.jl:1.0.0'
 
     input:
     tuple val(prefix), path(bam), path(bai), path(vcf)
diff --git a/modules/haplink/sequences/main.nf b/modules/haplink/sequences/main.nf
index fa1c76e..ed6f6a6 100644
--- a/modules/haplink/sequences/main.nf
+++ b/modules/haplink/sequences/main.nf
@@ -3,7 +3,7 @@ process HAPLINK_SEQUENCES {
     label 'process_single'
     label 'haplink'
 
-    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+    container 'ghcr.io/ksumngs/haplink.jl:1.0.0'
 
     input:
     tuple val(prefix), val(method), path(yaml)
diff --git a/modules/haplink/variants/main.nf b/modules/haplink/variants/main.nf
index ec6e9c8..f467f77 100644
--- a/modules/haplink/variants/main.nf
+++ b/modules/haplink/variants/main.nf
@@ -3,7 +3,7 @@ process HAPLINK_VARIANTS {
     label 'process_medium'
     label 'haplink'
 
-    container 'quay.io/biocontainers/haplink:1.0.0--h031d066_0'
+    container 'ghcr.io/ksumngs/haplink.jl:1.0.0'
 
     input:
     tuple val(prefix), path(bam), path(bai)