From 12d0ae03132906b038e49e9485d9a0a0ce15b92e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Mon, 2 Dec 2024 15:33:24 +0000
Subject: [PATCH 1/7] add files

---
 .../vt/decomposeblocksub/environment.yml      |  7 ++
 modules/nf-core/vt/decomposeblocksub/main.nf  | 65 +++++++++++++++++
 modules/nf-core/vt/decomposeblocksub/meta.yml | 51 +++++++++++++
 .../vt/decomposeblocksub/tests/main.nf.test   | 60 ++++++++++++++++
 .../decomposeblocksub/tests/main.nf.test.snap | 72 +++++++++++++++++++
 .../decomposeblocksub/tests/nextflow.config   |  6 ++
 6 files changed, 261 insertions(+)
 create mode 100644 modules/nf-core/vt/decomposeblocksub/environment.yml
 create mode 100644 modules/nf-core/vt/decomposeblocksub/main.nf
 create mode 100644 modules/nf-core/vt/decomposeblocksub/meta.yml
 create mode 100644 modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
 create mode 100644 modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/vt/decomposeblocksub/tests/nextflow.config

diff --git a/modules/nf-core/vt/decomposeblocksub/environment.yml b/modules/nf-core/vt/decomposeblocksub/environment.yml
new file mode 100644
index 00000000000..3f2cbb9b9e1
--- /dev/null
+++ b/modules/nf-core/vt/decomposeblocksub/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::vt=2015.11.10"
diff --git a/modules/nf-core/vt/decomposeblocksub/main.nf b/modules/nf-core/vt/decomposeblocksub/main.nf
new file mode 100644
index 00000000000..8d7aa506395
--- /dev/null
+++ b/modules/nf-core/vt/decomposeblocksub/main.nf
@@ -0,0 +1,65 @@
+process VT_DECOMPOSEBLOCKSUB {
+    tag "$meta.id"
+    label 'process_low'
+
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vt:2015.11.10--h5ef6573_4':
+        'biocontainers/vt:2015.11.10--h5ef6573_4' }"
+
+    input:
+    tuple val(meta), path(vcf), path(intervals)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")   , emit: vcf
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if ("$vcf" == "${prefix}.vcf" || "$vcf" == "${prefix}.vcf.gz") {
+        error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    }
+
+    def bed = intervals ? "-i ${intervals}" : ""
+    def VERSION = "2015.11.10" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    """
+    vt decompose_blocksub \\
+        -o ${prefix}.vcf \\
+        ${bed} \\
+        ${args} \\
+        ${vcf}
+
+    bgzip ${args2} --threads ${task.cpus} ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vt: ${VERSION}
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if ("$vcf" == "${prefix}.vcf" || "$vcf" == "${prefix}.vcf.gz") {
+        error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    }
+
+    def VERSION = "2015.11.10" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    """
+    touch ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vt: ${VERSION}
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/vt/decomposeblocksub/meta.yml b/modules/nf-core/vt/decomposeblocksub/meta.yml
new file mode 100644
index 00000000000..2400116ff9f
--- /dev/null
+++ b/modules/nf-core/vt/decomposeblocksub/meta.yml
@@ -0,0 +1,51 @@
+name: "vt_decomposeblocksub"
+description: Decomposes biallelic block substitutions into its constituent SNPs.
+keywords:
+  - decomposeblocksub
+  - multiallelic
+  - small variants
+  - snps
+  - indels
+  - block substitutions
+tools:
+  - "vt":
+      description: "A tool set for short variant discovery in genetic sequence data"
+      homepage: "https://genome.sph.umich.edu/wiki/Vt"
+      documentation: "https://genome.sph.umich.edu/wiki/Vt"
+      tool_dev_url: "https://github.com/atks/vt"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - vcf:
+        type: file
+        description: The VCF file to decompose
+        pattern: "*.vcf(.gz)?"
+    - intervals:
+        type: file
+        description: The intervals of the variants of decompose
+        pattern: "*.bed"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*.vcf.gz":
+          type: file
+          description: The decomposed VCF file
+          pattern: "*.vcf.gz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@kubranarci"
+maintainers:
+  - "@kubranarci"
diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
new file mode 100644
index 00000000000..8ca1713030d
--- /dev/null
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
@@ -0,0 +1,60 @@
+
+nextflow_process {
+
+    name "Test Process VT_DECOMPOSEBLOCKSUB"
+    script "../main.nf"
+    process "VT_DECOMPOSEBLOCKSUB"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vt"
+    tag "vt/decomposeblocksub"
+
+    test("test-vt-decomposeblocksub") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+				[]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-vt-decomposeblocksub-intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c3e5828d655
--- /dev/null
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test-vt-decomposeblocksub-intervals": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-02T15:31:33.067407198"
+    },
+    "test-vt-decomposeblocksub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decomposeblocksub.vcf.gz:md5,6dd85c7989b945dccb0a834c2c05407a"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-02T15:31:14.765445336"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vt/decomposeblocksub/tests/nextflow.config b/modules/nf-core/vt/decomposeblocksub/tests/nextflow.config
new file mode 100644
index 00000000000..c9c00888849
--- /dev/null
+++ b/modules/nf-core/vt/decomposeblocksub/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: VT_DECOMPOSEBLOCKSUB {
+        ext.prefix = "decomposeblocksub"
+        ext.args   = "-a"
+    }
+}

From dc6645379dd0b45a10afff98be85b25b158ec9c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Tue, 3 Dec 2024 09:41:40 +0000
Subject: [PATCH 2/7] versions fixed

---
 modules/nf-core/vt/decomposeblocksub/main.nf         | 12 +++---------
 .../vt/decomposeblocksub/tests/main.nf.test.snap     | 12 ++++++------
 2 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/modules/nf-core/vt/decomposeblocksub/main.nf b/modules/nf-core/vt/decomposeblocksub/main.nf
index 8d7aa506395..a7a72685602 100644
--- a/modules/nf-core/vt/decomposeblocksub/main.nf
+++ b/modules/nf-core/vt/decomposeblocksub/main.nf
@@ -28,20 +28,16 @@ process VT_DECOMPOSEBLOCKSUB {
     }
 
     def bed = intervals ? "-i ${intervals}" : ""
-    def VERSION = "2015.11.10" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-
     """
     vt decompose_blocksub \\
-        -o ${prefix}.vcf \\
+        -o ${prefix}.vcf.gz \\
         ${bed} \\
         ${args} \\
         ${vcf}
 
-    bgzip ${args2} --threads ${task.cpus} ${prefix}.vcf
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vt: ${VERSION}
+        vt: \$(echo \$(vt decompose_blocksub 2>&1 | grep 'decompose_blocksub v' | sed -n 's/.*decompose_blocksub v\\([0-9]\\+\\.[0-9]\\+\\).*/\\1/p' ))
     END_VERSIONS
     """
 
@@ -52,14 +48,12 @@ process VT_DECOMPOSEBLOCKSUB {
         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     }
 
-    def VERSION = "2015.11.10" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
-
     """
     touch ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vt: ${VERSION}
+        vt: \$(echo \$(vt decompose_blocksub 2>&1 | grep 'decompose_blocksub v' | sed -n 's/.*decompose_blocksub v\\([0-9]\\+\\.[0-9]\\+\\).*/\\1/p' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
index c3e5828d655..a5de36ab4d6 100644
--- a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
                 ],
                 "vcf": [
                     [
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
                 ]
             }
         ],
@@ -32,7 +32,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-02T15:31:33.067407198"
+        "timestamp": "2024-12-03T09:38:47.060601884"
     },
     "test-vt-decomposeblocksub": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
                 ],
                 "vcf": [
                     [
@@ -59,7 +59,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,befd56722087be88dc904c4096c02d66"
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
                 ]
             }
         ],
@@ -67,6 +67,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-02T15:31:14.765445336"
+        "timestamp": "2024-12-03T09:38:24.537448596"
     }
 }
\ No newline at end of file

From 3a03ca2f2691cd459a3bc716c78ae36994d522e8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Tue, 3 Dec 2024 15:44:49 +0000
Subject: [PATCH 3/7] added index and edam links

---
 modules/nf-core/vt/decomposeblocksub/main.nf  |  2 +-
 modules/nf-core/vt/decomposeblocksub/meta.yml | 12 +++++++
 .../vt/decomposeblocksub/tests/main.nf.test   |  2 ++
 .../decomposeblocksub/tests/main.nf.test.snap | 35 +++++++++++++++++++
 4 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/vt/decomposeblocksub/main.nf b/modules/nf-core/vt/decomposeblocksub/main.nf
index a7a72685602..78f71ded610 100644
--- a/modules/nf-core/vt/decomposeblocksub/main.nf
+++ b/modules/nf-core/vt/decomposeblocksub/main.nf
@@ -9,7 +9,7 @@ process VT_DECOMPOSEBLOCKSUB {
         'biocontainers/vt:2015.11.10--h5ef6573_4' }"
 
     input:
-    tuple val(meta), path(vcf), path(intervals)
+    tuple val(meta), path(vcf), path(index), path(intervals)
 
     output:
     tuple val(meta), path("*.vcf.gz")   , emit: vcf
diff --git a/modules/nf-core/vt/decomposeblocksub/meta.yml b/modules/nf-core/vt/decomposeblocksub/meta.yml
index 2400116ff9f..39d67b84ebb 100644
--- a/modules/nf-core/vt/decomposeblocksub/meta.yml
+++ b/modules/nf-core/vt/decomposeblocksub/meta.yml
@@ -25,10 +25,20 @@ input:
         type: file
         description: The VCF file to decompose
         pattern: "*.vcf(.gz)?"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016"
+    - index:
+        type: file
+        description: The VCF file to decompose
+        pattern: "*.tbi"
+        ontologies:
+          - edam: "http://edamontology.org/format_3616"
     - intervals:
         type: file
         description: The intervals of the variants of decompose
         pattern: "*.bed"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003"
 output:
   - vcf:
       - meta:
@@ -40,6 +50,8 @@ output:
           type: file
           description: The decomposed VCF file
           pattern: "*.vcf.gz"
+          ontologies:
+          - edam: "http://edamontology.org/format_3016"
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
index 8ca1713030d..f60517c10c1 100644
--- a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
@@ -19,6 +19,7 @@ nextflow_process {
                 input[0] = [
 				[ id:'test', single_end:false ], // meta map
 				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
 				[]
 				]
 
@@ -42,6 +43,7 @@ nextflow_process {
                 input[0] = [
 				[ id:'test', single_end:false ], // meta map
 				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
+                [],
 				file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
 				]
 
diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
index a5de36ab4d6..f4fe05fb153 100644
--- a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
@@ -1,4 +1,39 @@
 {
+    "test-vt-decomposeblocksub-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "/workspace/modules/.nf-test/tests/7c677eadb81135022105b896d444d040/work/dc/0626bebc1d6b4ceabc0e6f310f6df5/decomposeblocksub.vcf.gz"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "/workspace/modules/.nf-test/tests/7c677eadb81135022105b896d444d040/work/dc/0626bebc1d6b4ceabc0e6f310f6df5/decomposeblocksub.vcf.gz"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-03T15:34:17.433973974"
+    },
     "test-vt-decomposeblocksub-intervals": {
         "content": [
             {

From a64587dc3e71608681ebe4f728858ec2e9e29a0a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Tue, 3 Dec 2024 16:02:21 +0000
Subject: [PATCH 4/7] renew

---
 .../decomposeblocksub/tests/main.nf.test.snap | 35 -------------------
 1 file changed, 35 deletions(-)

diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
index f4fe05fb153..a5de36ab4d6 100644
--- a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test.snap
@@ -1,39 +1,4 @@
 {
-    "test-vt-decomposeblocksub-stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "/workspace/modules/.nf-test/tests/7c677eadb81135022105b896d444d040/work/dc/0626bebc1d6b4ceabc0e6f310f6df5/decomposeblocksub.vcf.gz"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "/workspace/modules/.nf-test/tests/7c677eadb81135022105b896d444d040/work/dc/0626bebc1d6b4ceabc0e6f310f6df5/decomposeblocksub.vcf.gz"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,2e541ec639f0458804a6cd3a58211f66"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-03T15:34:17.433973974"
-    },
     "test-vt-decomposeblocksub-intervals": {
         "content": [
             {

From e6131200577c7ed576b31b4ec0d537eb98e1aa6b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Wed, 4 Dec 2024 10:14:13 +0100
Subject: [PATCH 5/7] Update
 modules/nf-core/vt/decomposeblocksub/tests/main.nf.test

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
---
 modules/nf-core/vt/decomposeblocksub/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
index f60517c10c1..67b61ee3377 100644
--- a/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
+++ b/modules/nf-core/vt/decomposeblocksub/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				[ id:'test', single_end:false ], // meta map
+				    [ id:'test', single_end:false ], // meta map
 				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
 				[]

From 40996e0856b1cd3e2908d2a45a55ab2ed91fc185 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Wed, 4 Dec 2024 10:15:33 +0100
Subject: [PATCH 6/7] Update modules/nf-core/vt/decomposeblocksub/main.nf

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
---
 modules/nf-core/vt/decomposeblocksub/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/vt/decomposeblocksub/main.nf b/modules/nf-core/vt/decomposeblocksub/main.nf
index 78f71ded610..5b41eaa3c18 100644
--- a/modules/nf-core/vt/decomposeblocksub/main.nf
+++ b/modules/nf-core/vt/decomposeblocksub/main.nf
@@ -23,7 +23,7 @@ process VT_DECOMPOSEBLOCKSUB {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    if ("$vcf" == "${prefix}.vcf" || "$vcf" == "${prefix}.vcf.gz") {
+    if ("$vcf" == "${prefix}.vcf.gz") {
         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     }
 

From 0fa76cdf49480c0b556a7fa6a6f7a742bebb2a62 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Wed, 4 Dec 2024 10:15:54 +0100
Subject: [PATCH 7/7] Update modules/nf-core/vt/decomposeblocksub/main.nf

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
---
 modules/nf-core/vt/decomposeblocksub/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/vt/decomposeblocksub/main.nf b/modules/nf-core/vt/decomposeblocksub/main.nf
index 5b41eaa3c18..8bd77bcfe16 100644
--- a/modules/nf-core/vt/decomposeblocksub/main.nf
+++ b/modules/nf-core/vt/decomposeblocksub/main.nf
@@ -44,7 +44,7 @@ process VT_DECOMPOSEBLOCKSUB {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    if ("$vcf" == "${prefix}.vcf" || "$vcf" == "${prefix}.vcf.gz") {
+    if ("$vcf" == "${prefix}.vcf.gz") {
         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     }