From 95763975830bba162ba04359f019eab216ebc0ae Mon Sep 17 00:00:00 2001
From: stvdsomp <53609680+stvdsomp@users.noreply.github.com>
Date: Fri, 31 Jul 2026 10:06:13 +0200
Subject: [PATCH 1/6] add fna support for pbmm2

---
 modules/nf-core/pbmm2/align/main.nf | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/pbmm2/align/main.nf b/modules/nf-core/pbmm2/align/main.nf
index 3233b84df07f..69dc9787f5a3 100644
--- a/modules/nf-core/pbmm2/align/main.nf
+++ b/modules/nf-core/pbmm2/align/main.nf
@@ -23,10 +23,21 @@ process PBMM2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    fasta="${fasta}"
+    if [[ \${fasta} == *.fna ]]; then
+        new_name=\${fasta%.fna}.fa
+        mv \${fasta} \${new_name}
+        fasta=\${new_name}
+    elif [[ \${fasta} == *.fna.gz ]]; then
+        new_name=\${fasta%.fna.gz}.fa.gz
+        mv \${fasta} \${new_name}
+        fasta=\${new_name}
+    fi
+
     pbmm2 \\
         align \\
         $args \\
-        $fasta \\
+        \${fasta} \\
         $bam \\
         ${prefix}.bam \\
         --num-threads ${task.cpus}

From c4fb51766fe981cdb42a874910c3f5faa5e1990b Mon Sep 17 00:00:00 2001
From: stvdsomp <53609680+stvdsomp@users.noreply.github.com>
Date: Thu, 6 Aug 2026 11:31:50 +0200
Subject: [PATCH 2/6] add .fna support for pbmm2/align + test

---
 modules/nf-core/pbmm2/align/tests/fna.nf.test | 67 +++++++++++++++++++
 .../pbmm2/align/tests/fna.nf.test.snap        | 54 +++++++++++++++
 .../pbmm2/align/tests/main.nf.test.snap       |  6 +-
 3 files changed, 124 insertions(+), 3 deletions(-)
 create mode 100644 modules/nf-core/pbmm2/align/tests/fna.nf.test
 create mode 100644 modules/nf-core/pbmm2/align/tests/fna.nf.test.snap

diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test b/modules/nf-core/pbmm2/align/tests/fna.nf.test
new file mode 100644
index 000000000000..1867219fec4e
--- /dev/null
+++ b/modules/nf-core/pbmm2/align/tests/fna.nf.test
@@ -0,0 +1,67 @@
+nextflow_process {
+
+    name "Test Process PBMM2_ALIGN"
+    script "../main.nf"
+    process "PBMM2_ALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pbmm2"
+    tag "pbmm2/align"
+
+    test("pbmm2 - bam - fna") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("pbmm2 - bam - fna - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
new file mode 100644
index 000000000000..7df1b8b34817
--- /dev/null
+++ b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
@@ -0,0 +1,54 @@
+{
+    "pbmm2 - bam - fna": {
+        "content": [
+            {
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,f0f615a8a6172a739dfb81e6e08043f4"
+                    ]
+                ],
+                "versions_pbmm2": [
+                    [
+                        "PBMM2_ALIGN",
+                        "pbmm2",
+                        "26.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-06T11:28:10.82763057",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "pbmm2 - bam - fna - stub": {
+        "content": [
+            {
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_pbmm2": [
+                    [
+                        "PBMM2_ALIGN",
+                        "pbmm2",
+                        "26.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-06T11:28:15.998416537",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
index 8250bd5826be..4ada87e2eb32 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,f2be1fe20bbccf66afae237452e112cd"
+                        "test.bam:md5,ccb989e67933259d6213ca6236b7971c"
                     ]
                 ],
                 "versions_pbmm2": [
@@ -19,10 +19,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-01T15:03:18.017362993",
+        "timestamp": "2026-07-31T11:02:25.18889907",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.03.4"
+            "nextflow": "26.04.6"
         }
     },
     "pbmm2  - bam - stub": {

From 36c4229ab5aa0f1dab4991093020862895902a06 Mon Sep 17 00:00:00 2001
From: stvdsomp <53609680+stvdsomp@users.noreply.github.com>
Date: Thu, 6 Aug 2026 14:22:41 +0200
Subject: [PATCH 3/6] remove duplicate stub testing

---
 modules/nf-core/pbmm2/align/tests/fna.nf.test | 29 -------------------
 .../pbmm2/align/tests/fna.nf.test.snap        | 26 -----------------
 2 files changed, 55 deletions(-)

diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test b/modules/nf-core/pbmm2/align/tests/fna.nf.test
index 1867219fec4e..3a81512116bd 100644
--- a/modules/nf-core/pbmm2/align/tests/fna.nf.test
+++ b/modules/nf-core/pbmm2/align/tests/fna.nf.test
@@ -35,33 +35,4 @@ nextflow_process {
 
     }
 
-    test("pbmm2 - bam - fna - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
-                ]
-
-                input[1] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
-            )
-        }
-
-    }
-
 }
diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
index 7df1b8b34817..c3c119baa59c 100644
--- a/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
+++ b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
@@ -24,31 +24,5 @@
             "nf-test": "0.9.5",
             "nextflow": "26.04.6"
         }
-    },
-    "pbmm2 - bam - fna - stub": {
-        "content": [
-            {
-                "bam": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions_pbmm2": [
-                    [
-                        "PBMM2_ALIGN",
-                        "pbmm2",
-                        "26.2.0"
-                    ]
-                ]
-            }
-        ],
-        "timestamp": "2026-08-06T11:28:15.998416537",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "26.04.6"
-        }
     }
 }
\ No newline at end of file

From b1817eb4eb411bd2eb5ce49ff23945b5efd1219e Mon Sep 17 00:00:00 2001
From: stvdsomp <53609680+stvdsomp@users.noreply.github.com>
Date: Wed, 26 Aug 2026 10:03:53 +0200
Subject: [PATCH 4/6] moved new test into main.nf.test file

---
 modules/nf-core/pbmm2/align/tests/fna.nf.test | 38 -------------------
 .../pbmm2/align/tests/fna.nf.test.snap        | 28 --------------
 .../nf-core/pbmm2/align/tests/main.nf.test    | 28 +++++++++++++-
 .../pbmm2/align/tests/main.nf.test.snap       | 34 +++++++++++++++--
 4 files changed, 57 insertions(+), 71 deletions(-)
 delete mode 100644 modules/nf-core/pbmm2/align/tests/fna.nf.test
 delete mode 100644 modules/nf-core/pbmm2/align/tests/fna.nf.test.snap

diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test b/modules/nf-core/pbmm2/align/tests/fna.nf.test
deleted file mode 100644
index 3a81512116bd..000000000000
--- a/modules/nf-core/pbmm2/align/tests/fna.nf.test
+++ /dev/null
@@ -1,38 +0,0 @@
-nextflow_process {
-
-    name "Test Process PBMM2_ALIGN"
-    script "../main.nf"
-    process "PBMM2_ALIGN"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "pbmm2"
-    tag "pbmm2/align"
-
-    test("pbmm2 - bam - fna") {
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
-                ]
-
-                input[1] = [
-                    [ id:'test' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out)).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap b/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
deleted file mode 100644
index c3c119baa59c..000000000000
--- a/modules/nf-core/pbmm2/align/tests/fna.nf.test.snap
+++ /dev/null
@@ -1,28 +0,0 @@
-{
-    "pbmm2 - bam - fna": {
-        "content": [
-            {
-                "bam": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bam:md5,f0f615a8a6172a739dfb81e6e08043f4"
-                    ]
-                ],
-                "versions_pbmm2": [
-                    [
-                        "PBMM2_ALIGN",
-                        "pbmm2",
-                        "26.2.0"
-                    ]
-                ]
-            }
-        ],
-        "timestamp": "2026-08-06T11:28:10.82763057",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "26.04.6"
-        }
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test b/modules/nf-core/pbmm2/align/tests/main.nf.test
index ba365d81af40..b00a64d11ee4 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test
@@ -35,7 +35,33 @@ nextflow_process {
 
     }
 
-    test("pbmm2  - bam - stub") {
+    test("pbmm2 - bam - fna") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fna', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+    
+    test("pbmm2 - bam - stub") {
 
         options "-stub"
 
diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
index 4ada87e2eb32..55877ae9517e 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
@@ -19,13 +19,39 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-31T11:02:25.18889907",
+        "timestamp": "2026-08-26T09:48:54.607506251",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.6"
         }
     },
-    "pbmm2  - bam - stub": {
+    "pbmm2 - bam - fna": {
+        "content": [
+            {
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,f0f615a8a6172a739dfb81e6e08043f4"
+                    ]
+                ],
+                "versions_pbmm2": [
+                    [
+                        "PBMM2_ALIGN",
+                        "pbmm2",
+                        "26.2.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-26T09:49:01.229592637",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "pbmm2 - bam - stub": {
         "content": [
             {
                 "bam": [
@@ -45,10 +71,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-07-01T15:03:21.711112389",
+        "timestamp": "2026-08-26T09:49:08.199180076",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.03.4"
+            "nextflow": "26.04.6"
         }
     }
 }
\ No newline at end of file

From d2f598d69eba9d4f4f83f01903597f80ccb78d30 Mon Sep 17 00:00:00 2001
From: stvdsomp <53609680+stvdsomp@users.noreply.github.com>
Date: Wed, 26 Aug 2026 10:14:19 +0200
Subject: [PATCH 5/6] remove whitespace

---
 modules/nf-core/pbmm2/align/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test b/modules/nf-core/pbmm2/align/tests/main.nf.test
index a6b57ce7ab53..5fac28d120dc 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test
@@ -62,7 +62,7 @@ nextflow_process {
         }
 
     }
-    
+
     test("pbmm2 - bam - stub") {
 
         options "-stub"

From f8fc92ab5f00fb500d2ac9dc2fbf9e4a7612a934 Mon Sep 17 00:00:00 2001
From: stvdsomp <53609680+stvdsomp@users.noreply.github.com>
Date: Wed, 26 Aug 2026 11:20:17 +0200
Subject: [PATCH 6/6] update pbmm2 tests

---
 .../pbmm2/align/tests/main.nf.test.snap       | 24 +++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
index c7889cc5b9b0..4b465725fe36 100644
--- a/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
+++ b/modules/nf-core/pbmm2/align/tests/main.nf.test.snap
@@ -7,7 +7,15 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,ccb989e67933259d6213ca6236b7971c"
+                        "test.bam:md5,21fde9abeef32bf602d7e07521d6dd58"
+                    ]
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d19601b196d069d281c0280bbb6dda6f"
                     ]
                 ],
                 "versions_pbmm2": [
@@ -19,7 +27,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-08-26T09:48:54.607506251",
+        "timestamp": "2026-08-26T11:17:08.217985366",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.6"
@@ -33,7 +41,15 @@
                         {
                             "id": "test"
                         },
-                        "test.bam:md5,f0f615a8a6172a739dfb81e6e08043f4"
+                        "test.bam:md5,85fc597755dd2aca64e9141248fac2e0"
+                    ]
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d19601b196d069d281c0280bbb6dda6f"
                     ]
                 ],
                 "versions_pbmm2": [
@@ -45,7 +61,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-08-26T09:49:01.229592637",
+        "timestamp": "2026-08-26T11:17:26.093538311",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.6"