From 90951a6c3ea5eef686e8b9262de6e84cccd89d1a Mon Sep 17 00:00:00 2001
From: Max Cummins <mcummins@eit.org>
Date: Thu, 22 Jan 2026 14:09:29 +0000
Subject: [PATCH 1/2] migrate shovill module to topic versions

---
 modules/nf-core/shovill/main.nf            |  7 +-----
 modules/nf-core/shovill/meta.yml           | 27 +++++++++++++++++-----
 modules/nf-core/shovill/tests/main.nf.test |  8 +++----
 3 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf
index f92ce944ff2c..0d2f63383b2e 100644
--- a/modules/nf-core/shovill/main.nf
+++ b/modules/nf-core/shovill/main.nf
@@ -16,7 +16,7 @@ process SHOVILL {
     tuple val(meta), path("shovill.log")                        , emit: log
     tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
     tuple val(meta), path("contigs.{fastg,gfa,LastGraph}")      , optional:true, emit: gfa
-    path "versions.yml"                                         , emit: versions
+    tuple val("${task.process}"), val('shovill'), eval('shovill --version 2>&1 | sed "s/^.*shovill //"'), emit: versions_shovill, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,10 +33,5 @@ process SHOVILL {
         --ram $memory \\
         --outdir ./ \\
         --force
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/shovill/meta.yml b/modules/nf-core/shovill/meta.yml
index 0f14411b8e9b..6df19a614f20 100644
--- a/modules/nf-core/shovill/meta.yml
+++ b/modules/nf-core/shovill/meta.yml
@@ -79,13 +79,28 @@ output:
           pattern: "contigs.{fastg,gfa,LastGraph}"
           ontologies:
             - edam: http://edamontology.org/format_3975 # GFA 1
+  versions_shovill:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - shovill:
+          type: string
+          description: The name of the tool
+      - shovill --version 2>&1 | sed "s/^.*shovill //":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - shovill:
+          type: string
+          description: The name of the tool
+      - shovill --version 2>&1 | sed "s/^.*shovill //":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@rpetit3"
 maintainers:
diff --git a/modules/nf-core/shovill/tests/main.nf.test b/modules/nf-core/shovill/tests/main.nf.test
index 1f3d0917d67e..a65bc144e01b 100644
--- a/modules/nf-core/shovill/tests/main.nf.test
+++ b/modules/nf-core/shovill/tests/main.nf.test
@@ -25,7 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path(process.out.versions.get(0))).match() },
+                { assert process.out.findAll { key, val -> key.startsWith('versions') }},
                 { assert process.out.raw_contigs.size() == 1 },
                 { assert path(process.out.gfa.get(0).get(1)).readLines().any { it.contains("S") } },
                 { assert path(process.out.gfa.get(0).get(1)).readLines().any { it.contains("KC") } },
@@ -54,7 +54,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path(process.out.versions.get(0))).match() },
+                { assert process.out.findAll { key, val -> key.startsWith('versions') }},
                 { assert process.out.raw_contigs.size() == 1 },
                 { assert process.out.raw_contigs.get(0).get(1) ==~ ".*skesa.fasta" },
                 { assert path(process.out.raw_contigs.get(0).get(1)).readLines().any { it.contains(">Contig_1") } },
@@ -79,7 +79,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path(process.out.versions.get(0))).match() },
+                { assert process.out.findAll { key, val -> key.startsWith('versions') }},
                 { assert process.out.raw_contigs.size() == 1 },
                 { assert process.out.raw_contigs.get(0).get(1) ==~ ".*megahit.fasta" },
                 { assert path(process.out.raw_contigs.get(0).get(1)).readLines().any { it.contains("pilon") } }
@@ -103,7 +103,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(path(process.out.versions.get(0))).match() },
+                { assert process.out.findAll { key, val -> key.startsWith('versions') }},
                 { assert process.out.raw_contigs.size() == 1 },
                 { assert process.out.raw_contigs.get(0).get(1) ==~ ".*velvet.fasta" },
                 { assert path(process.out.raw_contigs.get(0).get(1)).readLines().any { it.contains("pilon") } }

From f8021772c9b9d9a6b8d9c0f51844b7b2878c1612 Mon Sep 17 00:00:00 2001
From: Max Cummins <mcummins@eit.org>
Date: Thu, 22 Jan 2026 14:17:17 +0000
Subject: [PATCH 2/2] add to authorship

---
 modules/nf-core/shovill/meta.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/shovill/meta.yml b/modules/nf-core/shovill/meta.yml
index 6df19a614f20..4bd43f8a8c05 100644
--- a/modules/nf-core/shovill/meta.yml
+++ b/modules/nf-core/shovill/meta.yml
@@ -103,5 +103,6 @@ topics:
           description: The expression to obtain the version of the tool
 authors:
   - "@rpetit3"
+  - "@eit-maxlcummins"
 maintainers:
   - "@rpetit3"