From 0265d4d857b3989f328a82140b9793e01c77682f Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Mon, 18 May 2026 18:16:11 +0100
Subject: [PATCH 01/12] Initial commit of TRF module

---
 modules/ensembl/features/trf/environment.yml |  5 +++
 modules/ensembl/features/trf/main.nf         | 43 ++++++++++++++++++++
 2 files changed, 48 insertions(+)
 create mode 100644 modules/ensembl/features/trf/environment.yml
 create mode 100644 modules/ensembl/features/trf/main.nf

diff --git a/modules/ensembl/features/trf/environment.yml b/modules/ensembl/features/trf/environment.yml
new file mode 100644
index 00000000..54eb1738
--- /dev/null
+++ b/modules/ensembl/features/trf/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - trf=4.09.1
\ No newline at end of file
diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
new file mode 100644
index 00000000..9dbb4227
--- /dev/null
+++ b/modules/ensembl/features/trf/main.nf
@@ -0,0 +1,43 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+process TANDEM_REPEATS_FINDER {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "quay.io/biocontainers/trf:4.09.1--h7b50bb2_7"
+
+    input:
+        tuple val(meta), path(fasta)
+
+    output:
+        tuple val(meta), path("*.dat"), emit: dat
+        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\.[0-9]+)+'"), emit: versions_trf, topic: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args task.ext.args ?: '2 7 7 80 10 100 500'
+        """
+        trf '${fasta}' ${args} -d -h
+        """
+
+    stub:
+        """
+        touch ${fasta.name}.dat
+        """
+}
\ No newline at end of file

From a43bd154ef8235bcaff8fc26287cba4502302376 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Mon, 18 May 2026 22:00:17 +0100
Subject: [PATCH 02/12] Update process name

---
 modules/ensembl/features/trf/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 9dbb4227..104b7faf 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -13,7 +13,7 @@
 // See the License for the specific language governing permissions and
 // limitations under the License.
 
-process TANDEM_REPEATS_FINDER {
+process FEATURES_TRF {
     tag "${meta.id}"
     label 'process_medium'
 

From d06160205cc81303ed1516384b7f27070416a53c Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Wed, 20 May 2026 11:09:06 +0100
Subject: [PATCH 03/12] Fix typo

---
 modules/ensembl/features/trf/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 104b7faf..868f562e 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -31,7 +31,7 @@ process FEATURES_TRF {
         task.ext.when == null || task.ext.when
 
     script:
-        def args task.ext.args ?: '2 7 7 80 10 100 500'
+        def args = task.ext.args ?: '2 7 7 80 10 100 500'
         """
         trf '${fasta}' ${args} -d -h
         """

From bd3a2491569226b03ede2e583a73211f7ca64c5e Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Wed, 17 Jun 2026 15:49:18 +0100
Subject: [PATCH 04/12] Add tests and meta

---
 modules/ensembl/features/trf/main.nf          |  8 ++-
 modules/ensembl/features/trf/meta.yml         | 67 +++++++++++++++++++
 .../ensembl/features/trf/tests/main.nf.test   | 49 ++++++++++++++
 3 files changed, 121 insertions(+), 3 deletions(-)
 create mode 100644 modules/ensembl/features/trf/meta.yml
 create mode 100644 modules/ensembl/features/trf/tests/main.nf.test

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 868f562e..da842749 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -25,7 +25,7 @@ process FEATURES_TRF {
 
     output:
         tuple val(meta), path("*.dat"), emit: dat
-        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\.[0-9]+)+'"), emit: versions_trf, topic: versions
+        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+' || echo 4.09.1"), emit: versions_trf, topic: versions
 
     when:
         task.ext.when == null || task.ext.when
@@ -38,6 +38,8 @@ process FEATURES_TRF {
 
     stub:
         """
-        touch ${fasta.name}.dat
+        cat > "${fasta.name}.dat" << 'EOF'
+        Sequence: ${fasta.name}
+        EOF
         """
-}
\ No newline at end of file
+}
diff --git a/modules/ensembl/features/trf/meta.yml b/modules/ensembl/features/trf/meta.yml
new file mode 100644
index 00000000..07ba48e5
--- /dev/null
+++ b/modules/ensembl/features/trf/meta.yml
@@ -0,0 +1,67 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "features_trf"
+description: Detect tandem repeats in FASTA sequences with Tandem Repeats Finder.
+keywords:
+  - fasta
+  - features
+  - repeats
+  - tandem repeats
+  - trf
+  - genomio
+tools:
+  - "trf":
+      description: "Tandem Repeats Finder detects and reports tandem repeats in DNA sequences."
+      homepage: "https://tandem.bu.edu/trf/trf.html"
+      documentation: "https://tandem.bu.edu/trf/trf.html"
+      tool_dev_url: "https://tandem.bu.edu/trf/trf.html"
+      licence: ["custom"]
+      identifier: "biotools:trf"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - fasta:
+        type: file
+        description: FASTA file containing DNA sequence(s)
+        pattern: "*.{fa,fasta,fna}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" # FASTA
+output:
+  dat:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.dat":
+          type: file
+          description: TRF repeat annotations in DAT format
+          pattern: "*.dat"
+  versions_trf:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - trf:
+          type: string
+          description: The tool name
+      - trf -v 2>&1 | grep -oE '[0-9]+(\.[0-9]+)+' || echo 4.09.1:
+          type: eval
+          description: The expression to obtain the TRF version
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - trf:
+          type: string
+          description: The tool name
+      - trf -v 2>&1 | grep -oE '[0-9]+(\.[0-9]+)+' || echo 4.09.1:
+          type: eval
+          description: The expression to obtain the TRF version
+authors:
+  - "ensembl-dev@ebi.ac.uk"
+maintainers:
+  - "ensembl-dev@ebi.ac.uk"
diff --git a/modules/ensembl/features/trf/tests/main.nf.test b/modules/ensembl/features/trf/tests/main.nf.test
new file mode 100644
index 00000000..ca06d4f0
--- /dev/null
+++ b/modules/ensembl/features/trf/tests/main.nf.test
@@ -0,0 +1,49 @@
+// See the NOTICE file distributed with this work for additional information
+// regarding copyright ownership.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+// nf-core modules test features/trf
+nextflow_process {
+
+    name "Test Process FEATURES_TRF"
+    script "../main.nf"
+    process "FEATURES_TRF"
+
+    tag "features"
+    tag "features/trf"
+
+    test("Stub: TRF") {
+        when {
+            options "-stub"
+
+            process {
+                """
+                input[0] = [[ id: 'test' ],file('dummy.fa')
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.dat.size() == 1 },
+                { assert process.out.dat[0][0] == [ id: 'test' ] },
+                { assert file(process.out.dat[0][1]).name == 'dummy.fa.dat' },
+                { assert file(process.out.dat[0][1]).size() > 0 },
+                { assert process.out.versions_trf.size() == 1 }
+            )
+        }
+    }
+}

From 174b29c5c969c4a66eaf653f55a702abf5d444b2 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Tue, 23 Jun 2026 11:36:05 +0100
Subject: [PATCH 05/12] Use TRF v4.10.0-rc2 to ensure 0 exit code on success

---
 modules/ensembl/features/trf/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index da842749..919abc2c 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -18,14 +18,14 @@ process FEATURES_TRF {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "quay.io/biocontainers/trf:4.09.1--h7b50bb2_7"
+    container "quay.io/biocontainers/trf:4.10.0rc2-0"
 
     input:
         tuple val(meta), path(fasta)
 
     output:
         tuple val(meta), path("*.dat"), emit: dat
-        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+' || echo 4.09.1"), emit: versions_trf, topic: versions
+        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0rc2-0"), emit: versions_trf, topic: versions
 
     when:
         task.ext.when == null || task.ext.when

From 445a68578d35c3c0d4e9b03e92ebbdda0770aca3 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Tue, 23 Jun 2026 11:58:10 +0100
Subject: [PATCH 06/12] Update container

---
 modules/ensembl/features/trf/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 919abc2c..979e1a47 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -18,7 +18,7 @@ process FEATURES_TRF {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "quay.io/biocontainers/trf:4.10.0rc2-0"
+    container "quay.io/biocontainers/trf:4.10.0rc2--h7b50bb2_0"
 
     input:
         tuple val(meta), path(fasta)

From 2ab2d8e4f2577e58681eb132c3a630c2f13639b9 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Thu, 25 Jun 2026 12:46:37 +0100
Subject: [PATCH 07/12] Refactor TRF arg input

---
 modules/ensembl/features/trf/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 979e1a47..484849ee 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -31,9 +31,9 @@ process FEATURES_TRF {
         task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: '2 7 7 80 10 100 500'
+        def args = task.ext.args ?: '2 7 7 80 10 100 500 -d -h'
         """
-        trf '${fasta}' ${args} -d -h
+        trf '${fasta}' ${args}
         """
 
     stub:

From fdd9434e8d3c3a94b4d59cbb1c6a821d1bbbb16d Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Thu, 25 Jun 2026 13:54:02 +0100
Subject: [PATCH 08/12] Test and versioning updates

---
 modules/ensembl/features/trf/main.nf          |  2 +-
 modules/ensembl/features/trf/meta.yml         |  4 +-
 .../ensembl/features/trf/tests/main.nf.test   | 15 +++----
 .../features/trf/tests/main.nf.test.snap      | 43 +++++++++++++++++++
 4 files changed, 53 insertions(+), 11 deletions(-)
 create mode 100644 modules/ensembl/features/trf/tests/main.nf.test.snap

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index 484849ee..a2eaa9e9 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -25,7 +25,7 @@ process FEATURES_TRF {
 
     output:
         tuple val(meta), path("*.dat"), emit: dat
-        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0rc2-0"), emit: versions_trf, topic: versions
+        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0rc2"), emit: versions_trf, topic: versions
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/features/trf/meta.yml b/modules/ensembl/features/trf/meta.yml
index 07ba48e5..2a989345 100644
--- a/modules/ensembl/features/trf/meta.yml
+++ b/modules/ensembl/features/trf/meta.yml
@@ -47,7 +47,7 @@ output:
       - trf:
           type: string
           description: The tool name
-      - trf -v 2>&1 | grep -oE '[0-9]+(\.[0-9]+)+' || echo 4.09.1:
+      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0-rc2:
           type: eval
           description: The expression to obtain the TRF version
 topics:
@@ -58,7 +58,7 @@ topics:
       - trf:
           type: string
           description: The tool name
-      - trf -v 2>&1 | grep -oE '[0-9]+(\.[0-9]+)+' || echo 4.09.1:
+      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0-rc2:
           type: eval
           description: The expression to obtain the TRF version
 authors:
diff --git a/modules/ensembl/features/trf/tests/main.nf.test b/modules/ensembl/features/trf/tests/main.nf.test
index ca06d4f0..348c575d 100644
--- a/modules/ensembl/features/trf/tests/main.nf.test
+++ b/modules/ensembl/features/trf/tests/main.nf.test
@@ -36,14 +36,13 @@ nextflow_process {
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert process.out.dat.size() == 1 },
-                { assert process.out.dat[0][0] == [ id: 'test' ] },
-                { assert file(process.out.dat[0][1]).name == 'dummy.fa.dat' },
-                { assert file(process.out.dat[0][1]).size() > 0 },
-                { assert process.out.versions_trf.size() == 1 }
-            )
+            assert process.success
+            assert snapshot(process.out).match()
+            assert process.out.dat.size() == 1
+            assert process.out.dat[0][0] == [ id: 'test' ]
+            assert file(process.out.dat[0][1]).name == 'dummy.fa.dat'
+            assert file(process.out.dat[0][1]).size() > 0
+            assert process.out.versions_trf.size() == 1
         }
     }
 }
diff --git a/modules/ensembl/features/trf/tests/main.nf.test.snap b/modules/ensembl/features/trf/tests/main.nf.test.snap
new file mode 100644
index 00000000..401f0329
--- /dev/null
+++ b/modules/ensembl/features/trf/tests/main.nf.test.snap
@@ -0,0 +1,43 @@
+{
+    "Stub: TRF": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917"
+                    ]
+                ],
+                "1": [
+                    [
+                        "FEATURES_TRF",
+                        "trf",
+                        "4.10.0rc2"
+                    ]
+                ],
+                "dat": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "dummy.fa.dat:md5,7afa5cc8da76212b28fe6a2c4db74917"
+                    ]
+                ],
+                "versions_trf": [
+                    [
+                        "FEATURES_TRF",
+                        "trf",
+                        "4.10.0rc2"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-25T13:50:41.590756",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    }
+}
\ No newline at end of file

From 13b3bbe31b418808ae6846ae2e75e02d8de04cd8 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Thu, 25 Jun 2026 14:07:32 +0100
Subject: [PATCH 09/12] Bump environment version

---
 modules/ensembl/features/trf/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/ensembl/features/trf/environment.yml b/modules/ensembl/features/trf/environment.yml
index 54eb1738..51431634 100644
--- a/modules/ensembl/features/trf/environment.yml
+++ b/modules/ensembl/features/trf/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - trf=4.09.1
\ No newline at end of file
+  - trf=4.10.0-rc2
\ No newline at end of file

From b843348325039f7775bf6d0ca8b9518ad811a2d2 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Thu, 25 Jun 2026 14:22:27 +0100
Subject: [PATCH 10/12] Fix TRF versions

---
 modules/ensembl/features/trf/main.nf                 | 2 +-
 modules/ensembl/features/trf/meta.yml                | 4 ++--
 modules/ensembl/features/trf/tests/main.nf.test.snap | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index a2eaa9e9..e9b16b77 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -25,7 +25,7 @@ process FEATURES_TRF {
 
     output:
         tuple val(meta), path("*.dat"), emit: dat
-        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0rc2"), emit: versions_trf, topic: versions
+        tuple val("${task.process}"), val('trf'), eval("trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0"), emit: versions_trf, topic: versions
 
     when:
         task.ext.when == null || task.ext.when
diff --git a/modules/ensembl/features/trf/meta.yml b/modules/ensembl/features/trf/meta.yml
index 2a989345..ea472367 100644
--- a/modules/ensembl/features/trf/meta.yml
+++ b/modules/ensembl/features/trf/meta.yml
@@ -47,7 +47,7 @@ output:
       - trf:
           type: string
           description: The tool name
-      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0-rc2:
+      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0:
           type: eval
           description: The expression to obtain the TRF version
 topics:
@@ -58,7 +58,7 @@ topics:
       - trf:
           type: string
           description: The tool name
-      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0-rc2:
+      - trf -v 2>&1 | grep -oE '[0-9]+(\\.[0-9]+)+(rc[0-9]+)?(-[0-9]+)?' || echo 4.10.0:
           type: eval
           description: The expression to obtain the TRF version
 authors:
diff --git a/modules/ensembl/features/trf/tests/main.nf.test.snap b/modules/ensembl/features/trf/tests/main.nf.test.snap
index 401f0329..7325e373 100644
--- a/modules/ensembl/features/trf/tests/main.nf.test.snap
+++ b/modules/ensembl/features/trf/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                     [
                         "FEATURES_TRF",
                         "trf",
-                        "4.10.0rc2"
+                        "4.10.0"
                     ]
                 ],
                 "dat": [
@@ -29,7 +29,7 @@
                     [
                         "FEATURES_TRF",
                         "trf",
-                        "4.10.0rc2"
+                        "4.10.0"
                     ]
                 ]
             }

From e66f12ef23a919f2425d49aa44a24f2b9a18b5c3 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Tue, 14 Jul 2026 13:10:22 +0100
Subject: [PATCH 11/12] TRF version fix

---
 modules/ensembl/features/trf/environment.yml | 2 +-
 modules/ensembl/features/trf/meta.yml        | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/ensembl/features/trf/environment.yml b/modules/ensembl/features/trf/environment.yml
index 51431634..202c4484 100644
--- a/modules/ensembl/features/trf/environment.yml
+++ b/modules/ensembl/features/trf/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - trf=4.10.0-rc2
\ No newline at end of file
+  - trf=4.10.0rc2
\ No newline at end of file
diff --git a/modules/ensembl/features/trf/meta.yml b/modules/ensembl/features/trf/meta.yml
index ea472367..043433c2 100644
--- a/modules/ensembl/features/trf/meta.yml
+++ b/modules/ensembl/features/trf/meta.yml
@@ -1,5 +1,4 @@
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "features_trf"
 description: Detect tandem repeats in FASTA sequences with Tandem Repeats Finder.
 keywords:

From 5ac0ebcb4b761aa9c5bab7ed5d73760ad336f533 Mon Sep 17 00:00:00 2001
From: Mark Quinton-Tulloch <markquintontulloch@gmail.com>
Date: Tue, 14 Jul 2026 13:17:24 +0100
Subject: [PATCH 12/12] Enforce -h option

---
 modules/ensembl/features/trf/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/ensembl/features/trf/main.nf b/modules/ensembl/features/trf/main.nf
index e9b16b77..475dba64 100644
--- a/modules/ensembl/features/trf/main.nf
+++ b/modules/ensembl/features/trf/main.nf
@@ -31,9 +31,9 @@ process FEATURES_TRF {
         task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: '2 7 7 80 10 100 500 -d -h'
+        def args = task.ext.args ?: '2 7 7 80 10 100 500 -d'
         """
-        trf '${fasta}' ${args}
+        trf '${fasta}' ${args} -h
         """
 
     stub: