From fcd2c3cb127dbb472c88a335767ef4d86ce2515f Mon Sep 17 00:00:00 2001
From: CormacKinsella <27350062+CormacKinsella@users.noreply.github.com>
Date: Fri, 27 Mar 2026 15:41:03 +0100
Subject: [PATCH 1/3] update biocontainer build

---
 modules/nf-core/merqury/merqury/environment.yml | 2 +-
 modules/nf-core/merqury/merqury/main.nf         | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/merqury/merqury/environment.yml b/modules/nf-core/merqury/merqury/environment.yml
index 84dc78d983b8..cd82819c39c8 100644
--- a/modules/nf-core/merqury/merqury/environment.yml
+++ b/modules/nf-core/merqury/merqury/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::merqury=1.3
+  - bioconda::merqury=1.3=hdfd78af_4
diff --git a/modules/nf-core/merqury/merqury/main.nf b/modules/nf-core/merqury/merqury/main.nf
index e1509ba02c1c..0fb81d3450d7 100644
--- a/modules/nf-core/merqury/merqury/main.nf
+++ b/modules/nf-core/merqury/merqury/main.nf
@@ -5,8 +5,8 @@ process MERQURY_MERQURY {
     // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_1':
-        'biocontainers/merqury:1.3--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/merqury:1.3--hdfd78af_4':
+        'biocontainers/merqury:1.3--hdfd78af_4' }"
 
     input:
     tuple val(meta), path(meryl_db), path(assembly)

From a75e5640aec69ea90992a6a1fbd90434449479a9 Mon Sep 17 00:00:00 2001
From: CormacKinsella <27350062+CormacKinsella@users.noreply.github.com>
Date: Fri, 27 Mar 2026 15:53:58 +0100
Subject: [PATCH 2/3] report meryl version also

---
 modules/nf-core/merqury/merqury/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/merqury/merqury/main.nf b/modules/nf-core/merqury/merqury/main.nf
index 0fb81d3450d7..71945aeecf6a 100644
--- a/modules/nf-core/merqury/merqury/main.nf
+++ b/modules/nf-core/merqury/merqury/main.nf
@@ -29,7 +29,8 @@ process MERQURY_MERQURY {
     tuple val(meta), path("*.hist.ploidy")       , emit: read_ploidy
     tuple val(meta), path("*.hapmers.blob.png")  , emit: hapmers_blob_png           , optional: true
     // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    tuple val("${task.process}"), val('merqury'), val('1.3'), emit: versions_merqury, topic: versions
+    tuple val("${task.process}"), val('merqury'), val('1.3')  , emit: versions_merqury, topic: versions
+    tuple val("${task.process}"), val('meryl')  , val('1.4.1'), emit: versions_meryl  , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From 0080cd7ac8bf9505e7f7cdda0937c76fd9889e94 Mon Sep 17 00:00:00 2001
From: CormacKinsella <27350062+CormacKinsella@users.noreply.github.com>
Date: Tue, 31 Mar 2026 12:32:13 +0200
Subject: [PATCH 3/3] revert additional version report

---
 modules/nf-core/merqury/merqury/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/nf-core/merqury/merqury/main.nf b/modules/nf-core/merqury/merqury/main.nf
index 71945aeecf6a..0fb81d3450d7 100644
--- a/modules/nf-core/merqury/merqury/main.nf
+++ b/modules/nf-core/merqury/merqury/main.nf
@@ -29,8 +29,7 @@ process MERQURY_MERQURY {
     tuple val(meta), path("*.hist.ploidy")       , emit: read_ploidy
     tuple val(meta), path("*.hapmers.blob.png")  , emit: hapmers_blob_png           , optional: true
     // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-    tuple val("${task.process}"), val('merqury'), val('1.3')  , emit: versions_merqury, topic: versions
-    tuple val("${task.process}"), val('meryl')  , val('1.4.1'), emit: versions_meryl  , topic: versions
+    tuple val("${task.process}"), val('merqury'), val('1.3'), emit: versions_merqury, topic: versions
 
     when:
     task.ext.when == null || task.ext.when