From 7020bca15ee5b984554aa703c1cae17599f1168b Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Tue, 26 May 2026 17:00:18 +0000
Subject: [PATCH 1/4] Remove space to trigger test

---
 modules/nf-core/pyclonevi/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/pyclonevi/main.nf b/modules/nf-core/pyclonevi/main.nf
index 0e63685c462..c3fe1eebc59 100644
--- a/modules/nf-core/pyclonevi/main.nf
+++ b/modules/nf-core/pyclonevi/main.nf
@@ -24,7 +24,6 @@ process PYCLONEVI {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     touch ${prefix}_cluster_table.csv
     touch ${prefix}.tsv

From 95cc7f07457a010bb8fa1dad140eea00aacbf063 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Wed, 27 May 2026 07:15:54 +0000
Subject: [PATCH 2/4] Update snapshot

---
 modules/nf-core/pyclonevi/tests/main.nf.test.snap | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/pyclonevi/tests/main.nf.test.snap b/modules/nf-core/pyclonevi/tests/main.nf.test.snap
index 31ad42db445..2c4794186a4 100644
--- a/modules/nf-core/pyclonevi/tests/main.nf.test.snap
+++ b/modules/nf-core/pyclonevi/tests/main.nf.test.snap
@@ -43,19 +43,19 @@
                     ]
                 ],
                 "versions_pyclonevi": [
-                    "versions.yml:md5,d7a72f90b5e871ad593d6b02ac78abb4"
+                    "versions.yml:md5,bc0f9ae69eb48d45a2c7389d55f7882e"
                 ]
             },
             {
                 "PYCLONEVI": {
-                    "pyclonevi": "0.1.6"
+                    "pyclonevi": "0.2.0"
                 }
             }
         ],
-        "timestamp": "2026-05-26T11:01:04.192976421",
+        "timestamp": "2026-05-26T17:22:45.350487609",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.2"
         }
     },
     "pyclonevi": {
@@ -105,14 +105,14 @@
                     ]
                 ],
                 "versions_pyclonevi": [
-                    "versions.yml:md5,764c065f67a1502d5158a8a018d8a388"
+                    "versions.yml:md5,3d517410bfd758e0eea9bef7f40d22e6"
                 ]
             }
         ],
-        "timestamp": "2026-05-26T11:00:56.527463061",
+        "timestamp": "2026-05-26T17:22:35.198094217",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.2"
         }
     }
 }
\ No newline at end of file

From 2c551446fb6d3b101e2965621382cab63c91c126 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Wed, 27 May 2026 07:59:21 +0000
Subject: [PATCH 3/4] Add .yaml

---
 modules/nf-core/pyclonevi/tests/main.nf.test      | 8 ++++----
 modules/nf-core/pyclonevi/tests/main.nf.test.snap | 7 ++++++-
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/pyclonevi/tests/main.nf.test b/modules/nf-core/pyclonevi/tests/main.nf.test
index d36b68c5657..2e95ca62b02 100644
--- a/modules/nf-core/pyclonevi/tests/main.nf.test
+++ b/modules/nf-core/pyclonevi/tests/main.nf.test
@@ -28,10 +28,10 @@ nextflow_process {
             assert process.success
             assertAll(
                 { assert snapshot(
-                    sanitizeOutput(
-                        process.out,
-                        unstableKeys: ["ctree_input", "pyclone_input", "pyclone_all_fits", "pyclone_best_fit"]
-                        )).match() }
+                    sanitizeOutput(process.out,
+                        unstableKeys: ["ctree_input", "pyclone_input", "pyclone_all_fits", "pyclone_best_fit"]),
+                    path(process.out.versions_pyclonevi[0]).yaml
+                    ).match() }
             )
         }
 
diff --git a/modules/nf-core/pyclonevi/tests/main.nf.test.snap b/modules/nf-core/pyclonevi/tests/main.nf.test.snap
index 2c4794186a4..32d2e825c6f 100644
--- a/modules/nf-core/pyclonevi/tests/main.nf.test.snap
+++ b/modules/nf-core/pyclonevi/tests/main.nf.test.snap
@@ -107,9 +107,14 @@
                 "versions_pyclonevi": [
                     "versions.yml:md5,3d517410bfd758e0eea9bef7f40d22e6"
                 ]
+            },
+            {
+                "PYCLONEVI": {
+                    "pyclonevi": "0.2.0"
+                }
             }
         ],
-        "timestamp": "2026-05-26T17:22:35.198094217",
+        "timestamp": "2026-05-27T07:54:19.275868186",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.2"

From bee30caabe4cd5ca50b006c949e0e7de87ecac0e Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Wed, 27 May 2026 08:53:39 +0000
Subject: [PATCH 4/4] Update python script version extraction

---
 modules/nf-core/pyclonevi/templates/main_script.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/nf-core/pyclonevi/templates/main_script.py b/modules/nf-core/pyclonevi/templates/main_script.py
index fd17532c272..1e88fc71aa4 100644
--- a/modules/nf-core/pyclonevi/templates/main_script.py
+++ b/modules/nf-core/pyclonevi/templates/main_script.py
@@ -163,9 +163,7 @@ def pyclone_ctree(joint, best_fit, ctree_input):
 
     # Version
     version = (
-        subprocess.check_output("pip show pyclone-vi | grep Version | awk '{print \$NF}'", shell=True)
-        .decode()
-        .split("\\n")[0]
+        subprocess.check_output("pyclone-vi --version | sed 's/.*version //g'", shell=True).decode().split("\\n")[0]
     )
 
     f = open("versions.yml", "a")