From 3a207b47c1d21895c72762fe72800a3581467fad Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Wed, 21 May 2025 14:12:02 +0200
Subject: [PATCH 1/9] Added module

---
 .pre-commit-config.yaml                       | 10 +-
 .../nf-core/msisensorpro/pro/environment.yml  |  7 ++
 modules/nf-core/msisensorpro/pro/main.nf      | 56 +++++++++++
 modules/nf-core/msisensorpro/pro/meta.yml     | 62 ++++++++++++
 .../msisensorpro/pro/tests/main.nf.test       | 99 +++++++++++++++++++
 .../msisensorpro/pro/tests/main.nf.test.snap  | 68 +++++++++++++
 6 files changed, 297 insertions(+), 5 deletions(-)
 create mode 100644 modules/nf-core/msisensorpro/pro/environment.yml
 create mode 100644 modules/nf-core/msisensorpro/pro/main.nf
 create mode 100644 modules/nf-core/msisensorpro/pro/meta.yml
 create mode 100644 modules/nf-core/msisensorpro/pro/tests/main.nf.test
 create mode 100644 modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 98c1d8ede8e..70574d3b948 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,13 +9,13 @@ repos:
         types: [yaml]
         additional_dependencies: ["ruamel.yaml"]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:
           - prettier@3.5.0
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.4
+    rev: 0.33.0
     hooks:
       - id: check-jsonschema
         name: "Match meta.ymls in one of the subdirectories of modules/nf-core"
@@ -36,20 +36,20 @@ repos:
 
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.3
+    rev: v0.11.10
     hooks:
       - id: ruff
         files: \.py$
         args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
       - id: ruff-format # formatter
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.2.1"
     hooks:
       - id: editorconfig-checker
         alias: ec
     # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
   - repo: https://github.com/hadolint/hadolint
-    rev: v2.12.0
+    rev: v2.13.1-beta
     hooks:
       - id: hadolint-docker
   - repo: https://github.com/nf-core/tools
diff --git a/modules/nf-core/msisensorpro/pro/environment.yml b/modules/nf-core/msisensorpro/pro/environment.yml
new file mode 100644
index 00000000000..3b66afc67ed
--- /dev/null
+++ b/modules/nf-core/msisensorpro/pro/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::msisensor-pro=1.3.0
diff --git a/modules/nf-core/msisensorpro/pro/main.nf b/modules/nf-core/msisensorpro/pro/main.nf
new file mode 100644
index 00000000000..84a186ff1f8
--- /dev/null
+++ b/modules/nf-core/msisensorpro/pro/main.nf
@@ -0,0 +1,56 @@
+process MSISENSORPRO_PRO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/msisensor-pro%3A1.3.0--hfef96ef_0':
+        'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
+
+    input:
+    tuple val(meta), path(cram)
+    path("${cram}.crai")
+    path(list)
+    path(fasta)
+    path("${fasta}.fai")
+
+    output:
+    tuple val(meta), path("${prefix}")          , emit: summary_msi
+    tuple val(meta), path("${prefix}_all")      , emit: all_msi
+    tuple val(meta), path("${prefix}_dis")      , emit: dis_msi
+    tuple val(meta), path("${prefix}_unstable") , emit: unstable_msi
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    msisensor-pro \\
+        pro \\
+        -d $list \\
+        -t $cram \\
+        -g $fasta \\
+        -o ${prefix} \\
+        -b $task.cpus \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        msisensorpro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\s*//p')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix} ${prefix}_all ${prefix}_dis ${prefix}_unstable
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        msisensorpro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\s*//p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/msisensorpro/pro/meta.yml b/modules/nf-core/msisensorpro/pro/meta.yml
new file mode 100644
index 00000000000..e3baadbae13
--- /dev/null
+++ b/modules/nf-core/msisensorpro/pro/meta.yml
@@ -0,0 +1,62 @@
+---
+name: "msisensorpro_pro"
+description: MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample
+  sequencing data
+keywords:
+  - msisensor-pro
+  - pro
+  - micro-satellite
+tools:
+  - msisensorpro:
+      description: Microsatellite Instability (MSI) detection using high-throughput
+        sequencing data.
+      homepage: https://github.com/xjtu-omics/msisensor-pro
+      documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
+      tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
+      doi: "10.1016/j.gpb.2020.02.001"
+      licence: ["Custom Licence"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - cram:
+        type: file
+        description: Sorted CRAM file
+        pattern: "*.{cram}"
+  - - list:
+        type: path
+        description: path to micro-satellite list
+  - - fasta:
+        type: path
+        description: path to reference genome used to create micro-satellite list
+        pattern: "*.{fasta}"
+output:
+  - - summary_msi:
+        type: file
+        description: txt file containing summary of results
+        pattern: "*.txt"
+  - - all_msi:
+        type: file
+        description: txt file containing all results
+        pattern: "*_all.txt"
+  - - dis_msi:
+        type: file
+        description: txt file containing the allele length distribution
+        pattern: "*_dis.txt"
+  - - unstable_msi:
+        type: file
+        description: txt file containing unstable micro-satellite sites
+        pattern: "*_unstable.txt"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@Tuur-ds"
+maintainers:
+  - "@Tuur-ds"
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
new file mode 100644
index 00000000000..1f770f7dfb5
--- /dev/null
+++ b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
@@ -0,0 +1,99 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test msisensorpro/pro
+nextflow_process {
+
+    name "Test Process MSISENSORPRO_PRO"
+    script "../main.nf"
+    process "MSISENSORPRO_PRO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "msisensorpro"
+    tag "msisensorpro/pro"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("testdata - [test, cram], list, fasta") {
+        setup {
+            run("MSISENSORPRO_SCAN") {
+                script "../../scan/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test'],
+                        file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta')
+                    ]
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ]
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai')
+                input[2] = MSISENSORPRO_SCAN.out.list.map{ it[1] }
+                input[3] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta')
+                input[4] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai')
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.summary_msi, process.out.all_msi, process.out.dis_msi, process.out.unstable_msi).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("testdata - stub - [test, cram], list, fasta") {
+
+        options "-stub"
+
+        setup {
+            run("MSISENSORPRO_SCAN") {
+                script "../../scan/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test', single_end:false ],
+                        file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ]
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai')
+                input[2] = MSISENSORPRO_SCAN.out.list.map{ it[1] }
+                input[3] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta')
+                input[4] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai')
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.summary_msi, process.out.all_msi, process.out.dis_msi, process.out.unstable_msi).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
new file mode 100644
index 00000000000..6ff0eea6226
--- /dev/null
+++ b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "testdata - stub - [test, cram], list, fasta": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_all:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_unstable:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-05-21T13:59:44.517502737"
+    },
+    "testdata - [test, cram], list, fasta": {
+        "content": [
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-05-21T11:22:31.003805747"
+    }
+}
\ No newline at end of file

From 98cacdd0b48ea1cbce260c7e48960dd6587e8a9f Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Wed, 21 May 2025 15:02:49 +0200
Subject: [PATCH 2/9] updated module

---
 .pre-commit-config.yaml                       | 10 +--
 modules/nf-core/msisensorpro/pro/main.nf      | 11 ++-
 .../msisensorpro/pro/tests/main.nf.test       | 51 +++++-------
 .../msisensorpro/pro/tests/main.nf.test.snap  | 82 +++++++++++++++++++
 4 files changed, 113 insertions(+), 41 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 70574d3b948..98c1d8ede8e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,13 +9,13 @@ repos:
         types: [yaml]
         additional_dependencies: ["ruamel.yaml"]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v4.0.0-alpha.8"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
         additional_dependencies:
           - prettier@3.5.0
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.33.0
+    rev: 0.29.4
     hooks:
       - id: check-jsonschema
         name: "Match meta.ymls in one of the subdirectories of modules/nf-core"
@@ -36,20 +36,20 @@ repos:
 
   # use ruff for python files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.10
+    rev: v0.7.3
     hooks:
       - id: ruff
         files: \.py$
         args: [--fix, --exit-non-zero-on-fix, "--select", "I,E1,E4,E7,E9,F,UP,N"] # sort imports and fix (rules taken from nf-core/tools)
       - id: ruff-format # formatter
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.2.1"
+    rev: "3.0.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
     # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
   - repo: https://github.com/hadolint/hadolint
-    rev: v2.13.1-beta
+    rev: v2.12.0
     hooks:
       - id: hadolint-docker
   - repo: https://github.com/nf-core/tools
diff --git a/modules/nf-core/msisensorpro/pro/main.nf b/modules/nf-core/msisensorpro/pro/main.nf
index 84a186ff1f8..1866bd9290e 100644
--- a/modules/nf-core/msisensorpro/pro/main.nf
+++ b/modules/nf-core/msisensorpro/pro/main.nf
@@ -8,11 +8,10 @@ process MSISENSORPRO_PRO {
         'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
 
     input:
-    tuple val(meta), path(cram)
-    path("${cram}.crai")
-    path(list)
-    path(fasta)
-    path("${fasta}.fai")
+    tuple val(meta), path(input), path(index)
+    tuple val(meta2), path(list)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(fai)
 
     output:
     tuple val(meta), path("${prefix}")          , emit: summary_msi
@@ -31,7 +30,7 @@ process MSISENSORPRO_PRO {
     msisensor-pro \\
         pro \\
         -d $list \\
-        -t $cram \\
+        -t $input \\
         -g $fasta \\
         -o ${prefix} \\
         -b $task.cpus \\
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
index 1f770f7dfb5..e7a4555fb52 100644
--- a/modules/nf-core/msisensorpro/pro/tests/main.nf.test
+++ b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
@@ -11,17 +11,13 @@ nextflow_process {
     tag "msisensorpro"
     tag "msisensorpro/pro"
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("testdata - [test, cram], list, fasta") {
+    test("testdata - [test, input, index], list, fasta") {
         setup {
             run("MSISENSORPRO_SCAN") {
                 script "../../scan/main.nf"
                 process {
                     """
-                    input[0] = [
-                        [ id:'test'],
-                        file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta')
-                    ]
+                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                     """
                 }
             }
@@ -30,13 +26,14 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                    [ id:'test_bam' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-                input[1] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai')
-                input[2] = MSISENSORPRO_SCAN.out.list.map{ it[1] }
-                input[3] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta')
-                input[4] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai')
+                input[1] = MSISENSORPRO_SCAN.out.list
+                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+
                 """
             }
         }
@@ -44,16 +41,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.summary_msi, process.out.all_msi, process.out.dis_msi, process.out.unstable_msi).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
-            )
+                { assert snapshot(process.out).match() }
+             )
         }
 
     }
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
-    test("testdata - stub - [test, cram], list, fasta") {
+    test("testdata - [test, input], list, fasta - stub") {
 
         options "-stub"
 
@@ -62,10 +56,7 @@ nextflow_process {
                 script "../../scan/main.nf"
                 process {
                     """
-                    input[0] = [
-                        [ id:'test', single_end:false ],
-                        file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
-                    ]
+                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                     """
                 }
             }
@@ -75,13 +66,14 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                    [ id:'test_bam' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-                input[1] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai')
-                input[2] = MSISENSORPRO_SCAN.out.list.map{ it[1] }
-                input[3] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta')
-                input[4] = file('https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai')
+                input[1] = MSISENSORPRO_SCAN.out.list
+                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+
                 """
             }
         }
@@ -89,8 +81,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.summary_msi, process.out.all_msi, process.out.dis_msi, process.out.unstable_msi).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
index 6ff0eea6226..af95fa554c5 100644
--- a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
+++ b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
@@ -1,4 +1,86 @@
 {
+    "testdata - [test, input], list, fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "all_msi": [
+                    
+                ],
+                "dis_msi": [
+                    
+                ],
+                "summary_msi": [
+                    
+                ],
+                "unstable_msi": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-05-21T14:44:05.883508584"
+    },
+    "testdata - [test, input, index], list, fasta": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    
+                ],
+                "all_msi": [
+                    
+                ],
+                "dis_msi": [
+                    
+                ],
+                "summary_msi": [
+                    
+                ],
+                "unstable_msi": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-05-21T14:43:59.904015128"
+    },
     "testdata - stub - [test, cram], list, fasta": {
         "content": [
             [

From 1e86c7e7ec5c36412c0692fc5d8d51923160c08f Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Wed, 21 May 2025 16:26:22 +0200
Subject: [PATCH 3/9] Updated testdata

---
 .../msisensorpro/pro/tests/main.nf.test       |  20 +--
 .../msisensorpro/pro/tests/main.nf.test.snap  | 124 ++++++++++++++----
 2 files changed, 112 insertions(+), 32 deletions(-)

diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
index e7a4555fb52..7c0b0ac07b8 100644
--- a/modules/nf-core/msisensorpro/pro/tests/main.nf.test
+++ b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 script "../../scan/main.nf"
                 process {
                     """
-                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
                     """
                 }
             }
@@ -27,12 +27,12 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test_bam' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true)
                 ]
                 input[1] = MSISENSORPRO_SCAN.out.list
-                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
-                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
+                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) ]
 
                 """
             }
@@ -56,7 +56,7 @@ nextflow_process {
                 script "../../scan/main.nf"
                 process {
                     """
-                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
                     """
                 }
             }
@@ -67,12 +67,12 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test_bam' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true)
                 ]
                 input[1] = MSISENSORPRO_SCAN.out.list
-                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
-                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
+                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) ]
 
                 """
             }
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
index af95fa554c5..0443511c7c8 100644
--- a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
+++ b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
@@ -3,34 +3,74 @@
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_all:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_unstable:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "4": [
-                    
+                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
                 ],
                 "all_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_all:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "dis_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "summary_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "unstable_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_unstable:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
                 ]
             }
         ],
@@ -38,40 +78,80 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-21T14:44:05.883508584"
+        "timestamp": "2025-05-21T16:23:24.356558342"
     },
     "testdata - [test, input, index], list, fasta": {
         "content": [
             {
                 "0": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam:md5,fd9bb39ab453ab41062a9cba4915e48c"
+                    ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_all:md5,8504b033b5e939b3cc5478baba649e76"
+                    ]
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_dis:md5,8e5ff0fd95ba6ea1167394af6ff3434e"
+                    ]
                 ],
                 "3": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_unstable:md5,2d3495f76e346a859190deaa5ac4357f"
+                    ]
                 ],
                 "4": [
-                    
+                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
                 ],
                 "all_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_all:md5,8504b033b5e939b3cc5478baba649e76"
+                    ]
                 ],
                 "dis_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_dis:md5,8e5ff0fd95ba6ea1167394af6ff3434e"
+                    ]
                 ],
                 "summary_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam:md5,fd9bb39ab453ab41062a9cba4915e48c"
+                    ]
                 ],
                 "unstable_msi": [
-                    
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_bam_unstable:md5,2d3495f76e346a859190deaa5ac4357f"
+                    ]
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
                 ]
             }
         ],
@@ -79,7 +159,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-21T14:43:59.904015128"
+        "timestamp": "2025-05-21T16:23:09.169763728"
     },
     "testdata - stub - [test, cram], list, fasta": {
         "content": [

From 680cfedb0f7ceb5384b4d9f9baedcb007b5e69e6 Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Wed, 21 May 2025 16:27:15 +0200
Subject: [PATCH 4/9] Updated msisensorpro to v1.3.0

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

diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf
index 265e6a132ad..edd27e83cb3 100644
--- a/modules/nf-core/msisensorpro/scan/main.nf
+++ b/modules/nf-core/msisensorpro/scan/main.nf
@@ -4,8 +4,8 @@ process MSISENSORPRO_SCAN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' :
-        'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }"
+            'https://depot.galaxyproject.org/singularity/msisensor-pro%3A1.3.0--hfef96ef_0':
+            'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
 
     input:
     tuple val(meta), path(fasta)

From a507fed6790dd907573558ee70b943f835aa186d Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Wed, 21 May 2025 16:34:12 +0200
Subject: [PATCH 5/9] Removed files for pro command

---
 .../nf-core/msisensorpro/pro/environment.yml  |   7 -
 modules/nf-core/msisensorpro/pro/main.nf      |  55 -----
 modules/nf-core/msisensorpro/pro/meta.yml     |  62 -----
 .../msisensorpro/pro/tests/main.nf.test       |  90 -------
 .../msisensorpro/pro/tests/main.nf.test.snap  | 230 ------------------
 5 files changed, 444 deletions(-)
 delete mode 100644 modules/nf-core/msisensorpro/pro/environment.yml
 delete mode 100644 modules/nf-core/msisensorpro/pro/main.nf
 delete mode 100644 modules/nf-core/msisensorpro/pro/meta.yml
 delete mode 100644 modules/nf-core/msisensorpro/pro/tests/main.nf.test
 delete mode 100644 modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap

diff --git a/modules/nf-core/msisensorpro/pro/environment.yml b/modules/nf-core/msisensorpro/pro/environment.yml
deleted file mode 100644
index 3b66afc67ed..00000000000
--- a/modules/nf-core/msisensorpro/pro/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - bioconda::msisensor-pro=1.3.0
diff --git a/modules/nf-core/msisensorpro/pro/main.nf b/modules/nf-core/msisensorpro/pro/main.nf
deleted file mode 100644
index 1866bd9290e..00000000000
--- a/modules/nf-core/msisensorpro/pro/main.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-process MSISENSORPRO_PRO {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/msisensor-pro%3A1.3.0--hfef96ef_0':
-        'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
-
-    input:
-    tuple val(meta), path(input), path(index)
-    tuple val(meta2), path(list)
-    tuple val(meta3), path(fasta)
-    tuple val(meta4), path(fai)
-
-    output:
-    tuple val(meta), path("${prefix}")          , emit: summary_msi
-    tuple val(meta), path("${prefix}_all")      , emit: all_msi
-    tuple val(meta), path("${prefix}_dis")      , emit: dis_msi
-    tuple val(meta), path("${prefix}_unstable") , emit: unstable_msi
-    path "versions.yml"                         , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    msisensor-pro \\
-        pro \\
-        -d $list \\
-        -t $input \\
-        -g $fasta \\
-        -o ${prefix} \\
-        -b $task.cpus \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        msisensorpro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\s*//p')
-    END_VERSIONS
-    """
-
-    stub:
-    prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix} ${prefix}_all ${prefix}_dis ${prefix}_unstable
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        msisensorpro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\s*//p')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/msisensorpro/pro/meta.yml b/modules/nf-core/msisensorpro/pro/meta.yml
deleted file mode 100644
index e3baadbae13..00000000000
--- a/modules/nf-core/msisensorpro/pro/meta.yml
+++ /dev/null
@@ -1,62 +0,0 @@
----
-name: "msisensorpro_pro"
-description: MSIsensor-pro/pro is a tool used to evaluate MSI using single (tumor) sample
-  sequencing data
-keywords:
-  - msisensor-pro
-  - pro
-  - micro-satellite
-tools:
-  - msisensorpro:
-      description: Microsatellite Instability (MSI) detection using high-throughput
-        sequencing data.
-      homepage: https://github.com/xjtu-omics/msisensor-pro
-      documentation: https://github.com/xjtu-omics/msisensor-pro/wiki
-      tool_dev_url: https://github.com/xjtu-omics/msisensor-pro
-      doi: "10.1016/j.gpb.2020.02.001"
-      licence: ["Custom Licence"]
-      identifier: ""
-
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1', single_end:false ]`
-    - cram:
-        type: file
-        description: Sorted CRAM file
-        pattern: "*.{cram}"
-  - - list:
-        type: path
-        description: path to micro-satellite list
-  - - fasta:
-        type: path
-        description: path to reference genome used to create micro-satellite list
-        pattern: "*.{fasta}"
-output:
-  - - summary_msi:
-        type: file
-        description: txt file containing summary of results
-        pattern: "*.txt"
-  - - all_msi:
-        type: file
-        description: txt file containing all results
-        pattern: "*_all.txt"
-  - - dis_msi:
-        type: file
-        description: txt file containing the allele length distribution
-        pattern: "*_dis.txt"
-  - - unstable_msi:
-        type: file
-        description: txt file containing unstable micro-satellite sites
-        pattern: "*_unstable.txt"
-  - versions:
-      - "versions.yml":
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
-authors:
-  - "@Tuur-ds"
-maintainers:
-  - "@Tuur-ds"
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test b/modules/nf-core/msisensorpro/pro/tests/main.nf.test
deleted file mode 100644
index 7c0b0ac07b8..00000000000
--- a/modules/nf-core/msisensorpro/pro/tests/main.nf.test
+++ /dev/null
@@ -1,90 +0,0 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test msisensorpro/pro
-nextflow_process {
-
-    name "Test Process MSISENSORPRO_PRO"
-    script "../main.nf"
-    process "MSISENSORPRO_PRO"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "msisensorpro"
-    tag "msisensorpro/pro"
-
-    test("testdata - [test, input, index], list, fasta") {
-        setup {
-            run("MSISENSORPRO_SCAN") {
-                script "../../scan/main.nf"
-                process {
-                    """
-                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
-                    """
-                }
-            }
-        }
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test_bam' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true)
-                ]
-                input[1] = MSISENSORPRO_SCAN.out.list
-                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
-                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) ]
-
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-             )
-        }
-
-    }
-
-    test("testdata - [test, input], list, fasta - stub") {
-
-        options "-stub"
-
-        setup {
-            run("MSISENSORPRO_SCAN") {
-                script "../../scan/main.nf"
-                process {
-                    """
-                    input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
-                    """
-                }
-            }
-        }
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test_bam' ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true)
-                ]
-                input[1] = MSISENSORPRO_SCAN.out.list
-                input[2] = [ [ id:'test_fasta' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]
-                input[3] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) ]
-
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
deleted file mode 100644
index 0443511c7c8..00000000000
--- a/modules/nf-core/msisensorpro/pro/tests/main.nf.test.snap
+++ /dev/null
@@ -1,230 +0,0 @@
-{
-    "testdata - [test, input], list, fasta - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_all:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_unstable:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
-                ],
-                "all_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_all:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "dis_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "summary_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "unstable_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_unstable:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-21T16:23:24.356558342"
-    },
-    "testdata - [test, input, index], list, fasta": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam:md5,fd9bb39ab453ab41062a9cba4915e48c"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_all:md5,8504b033b5e939b3cc5478baba649e76"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_dis:md5,8e5ff0fd95ba6ea1167394af6ff3434e"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_unstable:md5,2d3495f76e346a859190deaa5ac4357f"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
-                ],
-                "all_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_all:md5,8504b033b5e939b3cc5478baba649e76"
-                    ]
-                ],
-                "dis_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_dis:md5,8e5ff0fd95ba6ea1167394af6ff3434e"
-                    ]
-                ],
-                "summary_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam:md5,fd9bb39ab453ab41062a9cba4915e48c"
-                    ]
-                ],
-                "unstable_msi": [
-                    [
-                        {
-                            "id": "test_bam"
-                        },
-                        "test_bam_unstable:md5,2d3495f76e346a859190deaa5ac4357f"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,f44fd0e62f3a39a84a86006ac2a69011"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-21T16:23:09.169763728"
-    },
-    "testdata - stub - [test, cram], list, fasta": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_all:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_unstable:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-21T13:59:44.517502737"
-    },
-    "testdata - [test, cram], list, fasta": {
-        "content": [
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-05-21T11:22:31.003805747"
-    }
-}
\ No newline at end of file

From 3d7f71e1a38db3a94966a7dd67070b765e1b4b24 Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Thu, 22 May 2025 09:45:32 +0200
Subject: [PATCH 6/9] Updated snapshot

---
 .../msisensorpro/scan/tests/main.nf.test.snap | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/msisensorpro/scan/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/scan/tests/main.nf.test.snap
index f7ea66fc84e..0d5dd79b74e 100644
--- a/modules/nf-core/msisensorpro/scan/tests/main.nf.test.snap
+++ b/modules/nf-core/msisensorpro/scan/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e99820cdb69a600f5919ee1d7d5d1c3f"
+                    "versions.yml:md5,287e1f39989122a72b82ce521388c06b"
                 ],
                 "list": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e99820cdb69a600f5919ee1d7d5d1c3f"
+                    "versions.yml:md5,287e1f39989122a72b82ce521388c06b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-05T16:44:21.450285"
+        "timestamp": "2025-05-22T09:37:54.471663239"
     },
     "test-msisensorpro-scan": {
         "content": [
@@ -43,11 +43,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.msisensor_scan.list:md5,309d41b136993db24a9f3dade877753b"
+                        "test.msisensor_scan.list:md5,614754c7f1f44d5988dd80f8f21f69d1"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,e99820cdb69a600f5919ee1d7d5d1c3f"
+                    "versions.yml:md5,287e1f39989122a72b82ce521388c06b"
                 ],
                 "list": [
                     [
@@ -55,18 +55,18 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.msisensor_scan.list:md5,309d41b136993db24a9f3dade877753b"
+                        "test.msisensor_scan.list:md5,614754c7f1f44d5988dd80f8f21f69d1"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,e99820cdb69a600f5919ee1d7d5d1c3f"
+                    "versions.yml:md5,287e1f39989122a72b82ce521388c06b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-05T16:44:09.684249"
+        "timestamp": "2025-05-22T09:37:44.122010756"
     }
 }
\ No newline at end of file

From 5c2b31414d5eed67be4267d312aeb303c33032b5 Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Thu, 22 May 2025 10:00:44 +0200
Subject: [PATCH 7/9] Updated msisensorpro/msisomatic

---
 .../nf-core/msisensorpro/msisomatic/main.nf   |  8 +-
 .../msisomatic/tests/main.nf.test.snap        | 88 +++----------------
 2 files changed, 16 insertions(+), 80 deletions(-)

diff --git a/modules/nf-core/msisensorpro/msisomatic/main.nf b/modules/nf-core/msisensorpro/msisomatic/main.nf
index 796833c3d40..849179e631e 100644
--- a/modules/nf-core/msisensorpro/msisomatic/main.nf
+++ b/modules/nf-core/msisensorpro/msisomatic/main.nf
@@ -4,8 +4,8 @@ process MSISENSORPRO_MSISOMATIC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' :
-        'biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }"
+            'https://depot.galaxyproject.org/singularity/msisensor-pro%3A1.3.0--hfef96ef_0':
+            'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
 
     input:
     tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals)
@@ -15,8 +15,8 @@ process MSISENSORPRO_MSISOMATIC {
     output:
     tuple val(meta), path("${prefix}")         , emit: output_report
     tuple val(meta), path("${prefix}_dis")     , emit: output_dis
-    tuple val(meta), path("${prefix}_germline"), emit: output_germline
-    tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
+    // tuple val(meta), path("${prefix}_germline"), emit: output_germline
+    // tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
     path "versions.yml"                        , emit: versions
 
     when:
diff --git a/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap
index d809493cd3e..46c6d6c124f 100644
--- a/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap
+++ b/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test:md5,db7f2cc99ea79f79b0ba011c4bcbb43d"
+                        "test:md5,e72be74fca391a706f0dd77b8e35be71"
                     ]
                 ],
                 "1": [
@@ -15,42 +15,18 @@
                         {
                             "id": "test"
                         },
-                        "test_dis:md5,fc3e205b7ca50c9ecf3f70c87781e96f"
+                        "test_dis:md5,cbfcf8b5ce834ec2228c8f20fd6b424c"
                     ]
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_germline:md5,ba585b355c08877b8bca4901f49d9311"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_somatic:md5,836e617ddded07ec1e39089fd595c3d8"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,aa0b21daa2d1b75f211227f125236987"
+                    "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ],
                 "output_dis": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_dis:md5,fc3e205b7ca50c9ecf3f70c87781e96f"
-                    ]
-                ],
-                "output_germline": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_germline:md5,ba585b355c08877b8bca4901f49d9311"
+                        "test_dis:md5,cbfcf8b5ce834ec2228c8f20fd6b424c"
                     ]
                 ],
                 "output_report": [
@@ -58,19 +34,11 @@
                         {
                             "id": "test"
                         },
-                        "test:md5,db7f2cc99ea79f79b0ba011c4bcbb43d"
-                    ]
-                ],
-                "output_somatic": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_somatic:md5,836e617ddded07ec1e39089fd595c3d8"
+                        "test:md5,e72be74fca391a706f0dd77b8e35be71"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aa0b21daa2d1b75f211227f125236987"
+                    "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ]
             }
         ],
@@ -78,7 +46,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-14T22:11:35.572210341"
+        "timestamp": "2025-05-22T09:54:19.756315486"
     },
     "homo_sapiens - cram - fasta - list -- stub": {
         "content": [
@@ -100,23 +68,7 @@
                     ]
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_germline:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_somatic:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "4": [
-                    "versions.yml:md5,aa0b21daa2d1b75f211227f125236987"
+                    "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ],
                 "output_dis": [
                     [
@@ -126,14 +78,6 @@
                         "test_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "output_germline": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_germline:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
                 "output_report": [
                     [
                         {
@@ -142,21 +86,13 @@
                         "test:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "output_somatic": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_somatic:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
                 "versions": [
-                    "versions.yml:md5,aa0b21daa2d1b75f211227f125236987"
+                    "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ]
             },
             {
                 "MSISENSORPRO_MSISOMATIC": {
-                    "msisensor-pro": "1.2.0"
+                    "msisensor-pro": "1.3.0"
                 }
             }
         ],
@@ -164,6 +100,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-14T22:11:57.478582513"
+        "timestamp": "2025-05-22T09:54:30.972436147"
     }
-}
+}
\ No newline at end of file

From 6a1b94eebca847a634dbe38042a9eebb207140b2 Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Thu, 22 May 2025 10:07:41 +0200
Subject: [PATCH 8/9] Updated conda to v1.3.0, fixed linting

---
 modules/nf-core/msisensorpro/msisomatic/environment.yml | 2 +-
 modules/nf-core/msisensorpro/msisomatic/main.nf         | 2 +-
 modules/nf-core/msisensorpro/scan/environment.yml       | 2 +-
 modules/nf-core/msisensorpro/scan/main.nf               | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/msisensorpro/msisomatic/environment.yml b/modules/nf-core/msisensorpro/msisomatic/environment.yml
index f17216d6c5f..3b66afc67ed 100644
--- a/modules/nf-core/msisensorpro/msisomatic/environment.yml
+++ b/modules/nf-core/msisensorpro/msisomatic/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::msisensor-pro=1.2.0
+  - bioconda::msisensor-pro=1.3.0
diff --git a/modules/nf-core/msisensorpro/msisomatic/main.nf b/modules/nf-core/msisensorpro/msisomatic/main.nf
index 849179e631e..6291a5046ef 100644
--- a/modules/nf-core/msisensorpro/msisomatic/main.nf
+++ b/modules/nf-core/msisensorpro/msisomatic/main.nf
@@ -5,7 +5,7 @@ process MSISENSORPRO_MSISOMATIC {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
             'https://depot.galaxyproject.org/singularity/msisensor-pro%3A1.3.0--hfef96ef_0':
-            'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
+            'biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
 
     input:
     tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals)
diff --git a/modules/nf-core/msisensorpro/scan/environment.yml b/modules/nf-core/msisensorpro/scan/environment.yml
index f17216d6c5f..3b66afc67ed 100644
--- a/modules/nf-core/msisensorpro/scan/environment.yml
+++ b/modules/nf-core/msisensorpro/scan/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::msisensor-pro=1.2.0
+  - bioconda::msisensor-pro=1.3.0
diff --git a/modules/nf-core/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf
index edd27e83cb3..7ef4ae172c6 100644
--- a/modules/nf-core/msisensorpro/scan/main.nf
+++ b/modules/nf-core/msisensorpro/scan/main.nf
@@ -5,7 +5,7 @@ process MSISENSORPRO_SCAN {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
             'https://depot.galaxyproject.org/singularity/msisensor-pro%3A1.3.0--hfef96ef_0':
-            'quay.io/biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
+            'biocontainers/msisensor-pro:1.3.0--hfef96ef_0' }"
 
     input:
     tuple val(meta), path(fasta)

From ad44eef398a3a599159cbc39018869d8972ea1e9 Mon Sep 17 00:00:00 2001
From: Tuur-ds <tuur.de.sagher@student.howest.be>
Date: Thu, 22 May 2025 11:12:50 +0200
Subject: [PATCH 9/9] Added optional flag to germline and somatic output

---
 .../nf-core/msisensorpro/msisomatic/main.nf   |  4 +-
 .../msisomatic/tests/main.nf.test.snap        | 48 ++++++++++++++++++-
 2 files changed, 48 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/msisensorpro/msisomatic/main.nf b/modules/nf-core/msisensorpro/msisomatic/main.nf
index 6291a5046ef..41e8a04cfb4 100644
--- a/modules/nf-core/msisensorpro/msisomatic/main.nf
+++ b/modules/nf-core/msisensorpro/msisomatic/main.nf
@@ -15,8 +15,8 @@ process MSISENSORPRO_MSISOMATIC {
     output:
     tuple val(meta), path("${prefix}")         , emit: output_report
     tuple val(meta), path("${prefix}_dis")     , emit: output_dis
-    // tuple val(meta), path("${prefix}_germline"), emit: output_germline
-    // tuple val(meta), path("${prefix}_somatic") , emit: output_somatic
+    tuple val(meta), path("${prefix}_germline"), emit: output_germline, optional: true
+    tuple val(meta), path("${prefix}_somatic") , emit: output_somatic,  optional: true
     path "versions.yml"                        , emit: versions
 
     when:
diff --git a/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap b/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap
index 46c6d6c124f..9b65a6aa11d 100644
--- a/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap
+++ b/modules/nf-core/msisensorpro/msisomatic/tests/main.nf.test.snap
@@ -19,6 +19,12 @@
                     ]
                 ],
                 "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
                     "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ],
                 "output_dis": [
@@ -28,6 +34,9 @@
                         },
                         "test_dis:md5,cbfcf8b5ce834ec2228c8f20fd6b424c"
                     ]
+                ],
+                "output_germline": [
+                    
                 ],
                 "output_report": [
                     [
@@ -36,6 +45,9 @@
                         },
                         "test:md5,e72be74fca391a706f0dd77b8e35be71"
                     ]
+                ],
+                "output_somatic": [
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
@@ -46,7 +58,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-22T09:54:19.756315486"
+        "timestamp": "2025-05-22T11:04:58.705574319"
     },
     "homo_sapiens - cram - fasta - list -- stub": {
         "content": [
@@ -68,6 +80,22 @@
                     ]
                 ],
                 "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_germline:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_somatic:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
                     "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ],
                 "output_dis": [
@@ -78,6 +106,14 @@
                         "test_dis:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "output_germline": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_germline:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "output_report": [
                     [
                         {
@@ -86,6 +122,14 @@
                         "test:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "output_somatic": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_somatic:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,dcaf46d0c6a5501f318bc2b2797e4ba1"
                 ]
@@ -100,6 +144,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-05-22T09:54:30.972436147"
+        "timestamp": "2025-05-22T11:05:12.519069988"
     }
 }
\ No newline at end of file