From cf6a6286d80c42c0e704fd1f9412172893cfec30 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 10:45:36 +1100
Subject: [PATCH 01/31] feat(init): Commit inital meta.yml file

---
 .../nf-core/mmseqs/makepaddedseqdb/meta.yml   | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
new file mode 100644
index 000000000000..faba6881be80
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -0,0 +1,22 @@
+name: "mmseqs_makepaddedseqdb"
+description: Create an MMseqs padded database from an existing MMseqs database
+keywords:
+  - protein sequence
+  - databases
+  - clustering
+  - searching
+  - indexing
+  - mmseqs2
+tools:
+  - "mmseqs":
+      description: "MMseqs2: ultra fast and sensitive sequence search and clustering
+        suite"
+      homepage: "https://github.com/soedinglab/MMseqs2"
+      documentation: "https://mmseqs.com/latest/userguide.pdf"
+      tool_dev_url: "https://github.com/soedinglab/MMseqs2"
+      doi: "10.1093/bioinformatics/btw006"
+      licence:
+        - "GPL v3"
+      identifier: biotools:mmseqs
+authors:
+  - "@nbtm-sh"

From 4481c5df4304fab5ae27af572da7db12b033bb79 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 10:46:21 +1100
Subject: [PATCH 02/31] feat(env): add environment file

---
 modules/nf-core/mmseqs/makepaddedseqdb/environment.yml | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 modules/nf-core/mmseqs/makepaddedseqdb/environment.yml

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/environment.yml b/modules/nf-core/mmseqs/makepaddedseqdb/environment.yml
new file mode 100644
index 000000000000..072223f2aace
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::mmseqs2=18.8cc5c

From af5681b2c0cb7fbb93e24c7653818d7b50ba4456 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 10:56:07 +1100
Subject: [PATCH 03/31] feat(main): Add main boilerplate

---
 .../nf-core/mmseqs/makepaddedseqdb/main.nf    | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 modules/nf-core/mmseqs/makepaddedseqdb/main.nf

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
new file mode 100644
index 000000000000..048871c269ed
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -0,0 +1,23 @@
+process MMSEQS_MAKEPADDEDSEQDB {
+    tag "${meta.id}"
+    label 'process_low'
+    conda "${moduleDir}/environment.yml"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
+        : 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
+
+    input:
+    tuple val(meta), path(prefix)
+
+    script:
+    def args = task.ext.args ?: ''
+    padded_prefix = task.ext.prefix ?: "${meta.id}_padded"
+    """
+    mmseqs \\
+        makepaddedseqdb \\
+        ${prefix} \\
+        ${padded_prefix} \\
+        ${args}
+    """
+}

From baaeda9ee08ed1b1b907c3bd4afd7ff8ea4bc6c4 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 11:00:09 +1100
Subject: [PATCH 04/31] feat(ouptut): add output variables

---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index 048871c269ed..5f0e6bc68360 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -10,6 +10,10 @@ process MMSEQS_MAKEPADDEDSEQDB {
     input:
     tuple val(meta), path(prefix)
 
+    output:
+    tuple val(meta), path("${padded_prefix}/"), emit: db_padded
+    tuple val("${task.process}"), val('mmseqs'), eval('mmseqs version'), topic: versions, emit: versions_mmseqs
+
     script:
     def args = task.ext.args ?: ''
     padded_prefix = task.ext.prefix ?: "${meta.id}_padded"

From 7ec171a762d39aa93b6e9b0439a56ba12c592481 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 11:41:29 +1100
Subject: [PATCH 05/31] feat(stub): add stub

---
 .../nf-core/mmseqs/makepaddedseqdb/main.nf    | 21 +++++++++++++++++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index 5f0e6bc68360..23dfa1c66fee 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -13,15 +13,32 @@ process MMSEQS_MAKEPADDEDSEQDB {
     output:
     tuple val(meta), path("${padded_prefix}/"), emit: db_padded
     tuple val("${task.process}"), val('mmseqs'), eval('mmseqs version'), topic: versions, emit: versions_mmseqs
+    // targetdbpadded  targetdbpadded.dbtype  targetdbpadded.index  targetdbpadded.lookup  targetdbpadded_h  targetdbpadded_h.dbtype  targetdbpadded_h.index
 
     script:
     def args = task.ext.args ?: ''
     padded_prefix = task.ext.prefix ?: "${meta.id}_padded"
     """
+    mkdir -p ${padded_prefix}
     mmseqs \\
         makepaddedseqdb \\
-        ${prefix} \\
-        ${padded_prefix} \\
+        ${prefix}/${prefix} \\
+        ${padded_prefix}/${padded_prefix} \\
         ${args}
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    padded_prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+    mkdir -p ${padded_prefix}
+    touch ${padded_prefix}/${padded_prefix}
+    touch ${padded_prefix}/${padded_prefix}.dbtype
+    touch ${padded_prefix}/${padded_prefix}.index
+    touch ${padded_prefix}/${padded_prefix}.lookup
+    touch ${padded_prefix}/${padded_prefix}_h
+    touch ${padded_prefix}/${padded_prefix}_h.dbtype
+    touch ${padded_prefix}/${padded_prefix}_h.index
+    """
 }

From b75121d9982753106a2e900eb6460c599c28c38d Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 13:22:12 +1100
Subject: [PATCH 06/31] feat(meta): update meta to include output hints

---
 .../nf-core/mmseqs/makepaddedseqdb/meta.yml   | 40 +++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index faba6881be80..f1ec3ebb9874 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -18,5 +18,45 @@ tools:
       licence:
         - "GPL v3"
       identifier: biotools:mmseqs
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - sequence:
+        type: directory
+        description: Input of existing MMseqs database
+output:
+  db:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - ${prefix}_padded/:
+          type: directory
+          description: The padded MMseqs2 database
+  versions_mmseqs:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - mmseqs:
+          type: string
+          description: The name of the tool
+      - mmseqs version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - mmseqs:
+          type: string
+          description: The name of the tool
+      - mmseqs version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nbtm-sh"

From b5a638306ac7e47d6b889042651e24d457899b6a Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 14:19:31 +1100
Subject: [PATCH 07/31] feat(tests): add tests

---
 .../mmseqs/makepaddedseqdb/tests/main.nf.test | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
new file mode 100644
index 000000000000..5b2bdc807bd0
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -0,0 +1,45 @@
+nextflow_process {
+
+    name "Test Process MMSEQS_MAKEPADDEDSEQDB"
+    script "../main.nf"
+    process "MMSEQS_MAKEPADDEDSEQDB"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mmseqs"
+    tag "mmseqs/makepaddedseqdb"
+    tag "mmseqs/createdb"
+
+    setup {
+        run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_TARGET") {
+            script "../../../mmseqs/createdb/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test_query', single_end:true ], // meta map
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("Build padded database from existing cotigs database") {
+
+        when {
+            process {
+                """
+                input[0] = MMSEQS_CREATEDB_TARGET.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+                }
+            )
+        }
+
+    }
+}
+

From 067fa536ccc805600264fbee8efc6a4ab94f6d94 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 14:19:44 +1100
Subject: [PATCH 08/31] feat(test): add snapshot

---
 .../makepaddedseqdb/tests/main.nf.test.snap   | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
new file mode 100644
index 000000000000..0f319fec1765
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
@@ -0,0 +1,61 @@
+{
+    "Build padded database from existing cotigs database": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_query",
+                            "single_end": true
+                        },
+                        [
+                            "test_query_padded:md5,5b24585ba92fd826c78b8664c63b4e95",
+                            "test_query_padded.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
+                            "test_query_padded.index:md5,5946b4989d08320d9daca503155ba693",
+                            "test_query_padded.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
+                            "test_query_padded_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
+                            "test_query_padded_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_query_padded_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        "MMSEQS_MAKEPADDEDSEQDB",
+                        "mmseqs",
+                        "18.8cc5c"
+                    ]
+                ],
+                "db_padded": [
+                    [
+                        {
+                            "id": "test_query",
+                            "single_end": true
+                        },
+                        [
+                            "test_query_padded:md5,5b24585ba92fd826c78b8664c63b4e95",
+                            "test_query_padded.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
+                            "test_query_padded.index:md5,5946b4989d08320d9daca503155ba693",
+                            "test_query_padded.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
+                            "test_query_padded_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
+                            "test_query_padded_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_query_padded_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
+                        ]
+                    ]
+                ],
+                "versions_mmseqs": [
+                    [
+                        "MMSEQS_MAKEPADDEDSEQDB",
+                        "mmseqs",
+                        "18.8cc5c"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-24T14:18:06.618442817",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.6"
+        }
+    }
+}
\ No newline at end of file

From 8f8eb8939b69194a470b3f8b4dd9f7924990e275 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 14:21:13 +1100
Subject: [PATCH 09/31] feat(when): add when clause

---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index 23dfa1c66fee..b30f4b3cf7de 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -13,7 +13,9 @@ process MMSEQS_MAKEPADDEDSEQDB {
     output:
     tuple val(meta), path("${padded_prefix}/"), emit: db_padded
     tuple val("${task.process}"), val('mmseqs'), eval('mmseqs version'), topic: versions, emit: versions_mmseqs
-    // targetdbpadded  targetdbpadded.dbtype  targetdbpadded.index  targetdbpadded.lookup  targetdbpadded_h  targetdbpadded_h.dbtype  targetdbpadded_h.index
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''

From 64b8f563c51cbcc5fe3912d80870324abc4ca1f1 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 14:54:04 +1100
Subject: [PATCH 10/31] fix(meta): fix meta keys

---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index f1ec3ebb9874..1fb2c20f06ce 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -24,7 +24,7 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. `[ id:'test', single_end:false ]`
-    - sequence:
+    - prefix:
         type: directory
         description: Input of existing MMseqs database
 output:

From 5c142aca30e873bfc57ae80f1a26b5186d03e688 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 14:54:56 +1100
Subject: [PATCH 11/31] fix(meta): fix output keys

---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index 1fb2c20f06ce..acac950f6f30 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -28,7 +28,7 @@ input:
         type: directory
         description: Input of existing MMseqs database
 output:
-  db:
+  padded_db:
     - - meta:
           type: map
           description: |

From ee4876360a499d2aa03c9b59a28e70d83d299eb3 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 15:03:43 +1100
Subject: [PATCH 12/31] fix(meta): fix keys

---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index acac950f6f30..1b19e61c0f31 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -28,13 +28,13 @@ input:
         type: directory
         description: Input of existing MMseqs database
 output:
-  padded_db:
+  db_padded:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - ${prefix}_padded/:
+      - '${padded_prefix}/':
           type: directory
           description: The padded MMseqs2 database
   versions_mmseqs:

From 926f01c758a8f2754f2bb44528bba6ecc808b72e Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 15:23:51 +1100
Subject: [PATCH 13/31] fix(prek): fix syntax

---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml           | 2 +-
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index 1b19e61c0f31..c3357312e200 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -34,7 +34,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - '${padded_prefix}/':
+      - "${padded_prefix}/":
           type: directory
           description: The padded MMseqs2 database
   versions_mmseqs:
diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index 5b2bdc807bd0..9e422c49c3e0 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -42,4 +42,3 @@ nextflow_process {
 
     }
 }
-

From e766a2c6add228665694fb76be92852a4139a1fe Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 16:00:47 +1100
Subject: [PATCH 14/31] fix(padded): change from padded to gpu

---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index b30f4b3cf7de..5be015557c82 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -19,7 +19,7 @@ process MMSEQS_MAKEPADDEDSEQDB {
 
     script:
     def args = task.ext.args ?: ''
-    padded_prefix = task.ext.prefix ?: "${meta.id}_padded"
+    padded_prefix = task.ext.prefix ?: "${meta.id}_gpu"
     """
     mkdir -p ${padded_prefix}
     mmseqs \\
@@ -31,7 +31,7 @@ process MMSEQS_MAKEPADDEDSEQDB {
 
     stub:
     def args = task.ext.args ?: ''
-    padded_prefix = task.ext.prefix ?: "${meta.id}"
+    padded_prefix = task.ext.prefix ?: "${meta.id}_gpu"
     """
     echo ${args}
     mkdir -p ${padded_prefix}

From ef9c9bb97c5a9aa6bd65ace84fee927350896af8 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 16:01:54 +1100
Subject: [PATCH 15/31] fix(spelling): cotigs -> contigs

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

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index 9e422c49c3e0..2ddc32e86508 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_process {
         }
     }
 
-    test("Build padded database from existing cotigs database") {
+    test("Build padded database from existing contigs database") {
 
         when {
             process {

From 378fb740472516defc5f0ef8fc723a7a064c6cfc Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Tue, 24 Feb 2026 16:05:08 +1100
Subject: [PATCH 16/31] feat(snap): update snapshot with new paths

---
 .../makepaddedseqdb/tests/main.nf.test.snap   | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
index 0f319fec1765..cd34aebc598d 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Build padded database from existing cotigs database": {
+    "Build padded database from existing contigs database": {
         "content": [
             {
                 "0": [
@@ -9,13 +9,13 @@
                             "single_end": true
                         },
                         [
-                            "test_query_padded:md5,5b24585ba92fd826c78b8664c63b4e95",
-                            "test_query_padded.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
-                            "test_query_padded.index:md5,5946b4989d08320d9daca503155ba693",
-                            "test_query_padded.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
-                            "test_query_padded_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
-                            "test_query_padded_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
-                            "test_query_padded_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
+                            "test_query_gpu:md5,5b24585ba92fd826c78b8664c63b4e95",
+                            "test_query_gpu.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
+                            "test_query_gpu.index:md5,5946b4989d08320d9daca503155ba693",
+                            "test_query_gpu.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
+                            "test_query_gpu_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
+                            "test_query_gpu_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_query_gpu_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
                         ]
                     ]
                 ],
@@ -33,13 +33,13 @@
                             "single_end": true
                         },
                         [
-                            "test_query_padded:md5,5b24585ba92fd826c78b8664c63b4e95",
-                            "test_query_padded.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
-                            "test_query_padded.index:md5,5946b4989d08320d9daca503155ba693",
-                            "test_query_padded.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
-                            "test_query_padded_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
-                            "test_query_padded_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
-                            "test_query_padded_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
+                            "test_query_gpu:md5,5b24585ba92fd826c78b8664c63b4e95",
+                            "test_query_gpu.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
+                            "test_query_gpu.index:md5,5946b4989d08320d9daca503155ba693",
+                            "test_query_gpu.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
+                            "test_query_gpu_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
+                            "test_query_gpu_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_query_gpu_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
                         ]
                     ]
                 ],
@@ -52,7 +52,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-24T14:18:06.618442817",
+        "timestamp": "2026-02-24T16:04:29.291853095",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.6"

From 7705dc9ab0d564a643d79560f88de1e13c784087 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 08:58:19 +1100
Subject: [PATCH 17/31] fix(alias): remove alias

---
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index 2ddc32e86508..6d1be8ca203a 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_process {
     tag "mmseqs/createdb"
 
     setup {
-        run("MMSEQS_CREATEDB", alias: "MMSEQS_CREATEDB_TARGET") {
+        run("MMSEQS_CREATEDB") {
             script "../../../mmseqs/createdb/main.nf"
             process {
                 """
@@ -27,7 +27,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MMSEQS_CREATEDB_TARGET.out.db
+                input[0] = MMSEQS_CREATEDB.out.db
                 """
             }
         }

From 48fe89bf0b5f0b453b041b7ab0498ed055f5ff81 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:01:21 +1100
Subject: [PATCH 18/31] fix(naming): change from using reserved variable name

---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index 5be015557c82..b264fcbd018c 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -8,7 +8,7 @@ process MMSEQS_MAKEPADDEDSEQDB {
         : 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
 
     input:
-    tuple val(meta), path(prefix)
+    tuple val(meta), path(db_in)
 
     output:
     tuple val(meta), path("${padded_prefix}/"), emit: db_padded
@@ -24,7 +24,7 @@ process MMSEQS_MAKEPADDEDSEQDB {
     mkdir -p ${padded_prefix}
     mmseqs \\
         makepaddedseqdb \\
-        ${prefix}/${prefix} \\
+        ${db_in}/${db_in} \\
         ${padded_prefix}/${padded_prefix} \\
         ${args}
     """

From cbe569afbe6ea2590f35df9612e48b38e6a774f4 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:07:14 +1100
Subject: [PATCH 19/31] Update
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
---
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index 6d1be8ca203a..4aa5e63dc870 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
             script "../../../mmseqs/createdb/main.nf"
             process {
                 """
-                input[0] = [ [ id:'test_query', single_end:true ], // meta map
+                input[0] = [ [ id:'test_query' ], 
                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
                 ]
                 """

From 22230fb256d8c38d3a62935a2912887ab1a70691 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:07:34 +1100
Subject: [PATCH 20/31] Update
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
---
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index 4aa5e63dc870..072ce46917a2 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -35,7 +35,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match()
+                { assert snapshot(sanitizeOutput(process.out)).match()
                 }
             )
         }

From ab8bf25155630e2813a1a376d59ba8ba0d8318e1 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:08:08 +1100
Subject: [PATCH 21/31] Update
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
---
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index 072ce46917a2..b1a6681b247d 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_process {
         }
     }
 
-    test("Build padded database from existing contigs database") {
+    test("mmseqs_db sarscov2 contigs") {
 
         when {
             process {

From daf292cc5470b3e479f3d67f2568464290e5c6f5 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:08:50 +1100
Subject: [PATCH 22/31] Update modules/nf-core/mmseqs/makepaddedseqdb/main.nf

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index b264fcbd018c..f61c479c14aa 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -19,7 +19,7 @@ process MMSEQS_MAKEPADDEDSEQDB {
 
     script:
     def args = task.ext.args ?: ''
-    padded_prefix = task.ext.prefix ?: "${meta.id}_gpu"
+     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir -p ${padded_prefix}
     mmseqs \\

From eeda6d4902574c07b874d0675326a91551382b46 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:09:34 +1100
Subject: [PATCH 23/31] Update modules/nf-core/mmseqs/makepaddedseqdb/main.nf

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index f61c479c14aa..2ae8371f1052 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -20,6 +20,9 @@ process MMSEQS_MAKEPADDEDSEQDB {
     script:
     def args = task.ext.args ?: ''
      def prefix = task.ext.prefix ?: "${meta.id}"
+        if ("${db_in}" == "${prefix}") {
+          error("Input and output names of databases are the same, set prefix in module configuration to disambiguate!")
+      }
     """
     mkdir -p ${padded_prefix}
     mmseqs \\

From 3dd6da4d85ff9046836cf797073f99b268f37777 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 09:10:23 +1100
Subject: [PATCH 24/31] Update modules/nf-core/mmseqs/makepaddedseqdb/meta.yml

Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index c3357312e200..4afbdd81bc9c 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -34,7 +34,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - "${padded_prefix}/":
+      - "${prefix}/":
           type: directory
           description: The padded MMseqs2 database
   versions_mmseqs:

From c875e024e7db89d609c7226b62a086929eebca2f Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 10:39:14 +1100
Subject: [PATCH 25/31] fix(output): fix db output to use set prefix

---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index 2ae8371f1052..d26b543965b1 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -11,7 +11,7 @@ process MMSEQS_MAKEPADDEDSEQDB {
     tuple val(meta), path(db_in)
 
     output:
-    tuple val(meta), path("${padded_prefix}/"), emit: db_padded
+    tuple val(meta), path("${prefix}/"), emit: db_padded
     tuple val("${task.process}"), val('mmseqs'), eval('mmseqs version'), topic: versions, emit: versions_mmseqs
 
     when:
@@ -19,16 +19,18 @@ process MMSEQS_MAKEPADDEDSEQDB {
 
     script:
     def args = task.ext.args ?: ''
-     def prefix = task.ext.prefix ?: "${meta.id}"
-        if ("${db_in}" == "${prefix}") {
-          error("Input and output names of databases are the same, set prefix in module configuration to disambiguate!")
-      }
+    def args2 = task.ext.args2 ?: '*.dbtype'
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("${db_in}" == "${prefix}") {
+        error("Input and output names of databases are the same, set prefix in module configuration to disambiguate!")
+    }
     """
-    mkdir -p ${padded_prefix}
+    DB_TARGET_PATH_NAME=\$(find -L "${db_in}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
+    mkdir -p ${prefix}
     mmseqs \\
         makepaddedseqdb \\
-        ${db_in}/${db_in} \\
-        ${padded_prefix}/${padded_prefix} \\
+        \$DB_TARGET_PATH_NAME \\
+        ${prefix}/${prefix} \\
         ${args}
     """
 

From fbddba58c4bbe1dd865ec4ce2b3ea7cd86ec804d Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 10:39:54 +1100
Subject: [PATCH 26/31] fix(meta): fix meta yml

---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index 4afbdd81bc9c..a1ef41ab595a 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -24,7 +24,7 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. `[ id:'test', single_end:false ]`
-    - prefix:
+    - db_in:
         type: directory
         description: Input of existing MMseqs database
 output:

From 15af087ca02e72299020f68716f757d9412ab387 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 10:40:23 +1100
Subject: [PATCH 27/31] feat(test): add config variable to tests

---
 modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
index b1a6681b247d..6c3ae4b7ea60 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -9,12 +9,14 @@ nextflow_process {
     tag "mmseqs/makepaddedseqdb"
     tag "mmseqs/createdb"
 
+    config "./nextflow.config"
+
     setup {
         run("MMSEQS_CREATEDB") {
             script "../../../mmseqs/createdb/main.nf"
             process {
                 """
-                input[0] = [ [ id:'test_query' ], 
+                input[0] = [ [ id:'test_query' ],
                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
                 ]
                 """
@@ -25,6 +27,9 @@ nextflow_process {
     test("mmseqs_db sarscov2 contigs") {
 
         when {
+            params {
+                module_prefix = "test_query_gpu"
+            }
             process {
                 """
                 input[0] = MMSEQS_CREATEDB.out.db

From afd890474647f3c103a8eda4110976cef44dd107 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 10:40:59 +1100
Subject: [PATCH 28/31] fix(snapshot): update snapshot to use new variable
 names

---
 .../makepaddedseqdb/tests/main.nf.test.snap   | 31 ++-----------------
 1 file changed, 3 insertions(+), 28 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
index cd34aebc598d..8ce6f93de878 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
@@ -1,36 +1,11 @@
 {
-    "Build padded database from existing contigs database": {
+    "mmseqs_db sarscov2 contigs": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test_query",
-                            "single_end": true
-                        },
-                        [
-                            "test_query_gpu:md5,5b24585ba92fd826c78b8664c63b4e95",
-                            "test_query_gpu.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
-                            "test_query_gpu.index:md5,5946b4989d08320d9daca503155ba693",
-                            "test_query_gpu.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
-                            "test_query_gpu_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
-                            "test_query_gpu_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
-                            "test_query_gpu_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        "MMSEQS_MAKEPADDEDSEQDB",
-                        "mmseqs",
-                        "18.8cc5c"
-                    ]
-                ],
                 "db_padded": [
                     [
                         {
-                            "id": "test_query",
-                            "single_end": true
+                            "id": "test_query"
                         },
                         [
                             "test_query_gpu:md5,5b24585ba92fd826c78b8664c63b4e95",
@@ -52,7 +27,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-02-24T16:04:29.291853095",
+        "timestamp": "2026-02-25T10:33:19.910807101",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.04.6"

From c034130371771def722809d79321fed1871e340c Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 10:41:27 +1100
Subject: [PATCH 29/31] feat(commit): add commit to add prefix variable

---
 modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config b/modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config
new file mode 100644
index 000000000000..735a3eb0904f
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "MMSEQS_MAKEPADDEDSEQDB" {
+        ext.prefix = params.module_prefix
+    }
+}

From be265225bcd208959d4037fa0e4fc8e17fb61960 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Wed, 25 Feb 2026 10:48:47 +1100
Subject: [PATCH 30/31] fix(stub): fix stub run to use prefix instead of
 prefix_padded

---
 modules/nf-core/mmseqs/makepaddedseqdb/main.nf | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
index d26b543965b1..61857c179f67 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -36,16 +36,16 @@ process MMSEQS_MAKEPADDEDSEQDB {
 
     stub:
     def args = task.ext.args ?: ''
-    padded_prefix = task.ext.prefix ?: "${meta.id}_gpu"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo ${args}
-    mkdir -p ${padded_prefix}
-    touch ${padded_prefix}/${padded_prefix}
-    touch ${padded_prefix}/${padded_prefix}.dbtype
-    touch ${padded_prefix}/${padded_prefix}.index
-    touch ${padded_prefix}/${padded_prefix}.lookup
-    touch ${padded_prefix}/${padded_prefix}_h
-    touch ${padded_prefix}/${padded_prefix}_h.dbtype
-    touch ${padded_prefix}/${padded_prefix}_h.index
+    mkdir -p ${prefix}
+    touch ${prefix}/${prefix}
+    touch ${prefix}/${prefix}.dbtype
+    touch ${prefix}/${prefix}.index
+    touch ${prefix}/${prefix}.lookup
+    touch ${prefix}/${prefix}_h
+    touch ${prefix}/${prefix}_h.dbtype
+    touch ${prefix}/${prefix}_h.index
     """
 }

From 49beaacc33a7db99b88b5f6176069672fdccb241 Mon Sep 17 00:00:00 2001
From: nbtm-sh <nathan@nbti.net>
Date: Thu, 26 Feb 2026 09:06:02 +1100
Subject: [PATCH 31/31] feat(meta): add myself as a maintainer

---
 modules/nf-core/mmseqs/makepaddedseqdb/meta.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
index a1ef41ab595a..8858d9bb9908 100644
--- a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -60,3 +60,5 @@ topics:
           description: The expression to obtain the version of the tool
 authors:
   - "@nbtm-sh"
+maintainers:
+  - "@nbtm-sh"