From 9c1f1d7360afb902ff931a21957651534e8b34ca Mon Sep 17 00:00:00 2001
From: Felix Lenner <felix.lenner@igp.uu.se>
Date: Tue, 9 Jul 2024 14:49:23 +0000
Subject: [PATCH] Fix bcftools plugin split

---
 modules/nf-core/bcftools/pluginsplit/main.nf  |  20 +-
 .../bcftools/pluginsplit/tests/main.nf.test   | 188 +++++++++
 .../pluginsplit/tests/main.nf.test.snap       | 356 ++++++++++++++++++
 .../pluginsplit/tests/nextflow.config         |   5 +
 .../bcftools/pluginsplit/tests/tags.yml       |   2 +
 tests/config/pytest_modules.yml               |   3 -
 .../nf-core/bcftools/pluginsplit/main.nf      |  48 ---
 .../bcftools/pluginsplit/nextflow.config      |   5 -
 .../nf-core/bcftools/pluginsplit/test.yml     |  23 --
 9 files changed, 565 insertions(+), 85 deletions(-)
 create mode 100644 modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
 create mode 100644 modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/bcftools/pluginsplit/tests/nextflow.config
 create mode 100644 modules/nf-core/bcftools/pluginsplit/tests/tags.yml
 delete mode 100644 tests/modules/nf-core/bcftools/pluginsplit/main.nf
 delete mode 100644 tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
 delete mode 100644 tests/modules/nf-core/bcftools/pluginsplit/test.yml

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 83de8f966d5b..082802be7095 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -15,8 +15,10 @@ process BCFTOOLS_PLUGINSPLIT {
     path(targets)
 
     output:
-    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}")  , emit: vcf
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")                    , emit: csi, optional: true
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,6 +34,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     """
     bcftools plugin split \\
+        ${args} \\
         ${vcf} \\
         ${samples_arg} \\
         ${groups_arg} \\
@@ -56,12 +59,17 @@ process BCFTOOLS_PLUGINSPLIT {
                 args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                 args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                 "vcf"
-
+    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                args.contains("--write-index") || args.contains("-W") ? "csi" :
+                ""
     def determination_file = samples ?: targets
+    def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
+    def create_files = "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt; while IFS= read -r filename; do ${create_cmd} \"\$filename\"; done < files.txt"
+    def create_index = index.matches("csi|tbi") ? "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}.${index}/' > indices.txt; touch \$(<indices.txt)" : ""
     """
-    cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
-
-    touch \$(<files.txt)
+    ${create_files}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
new file mode 100644
index 000000000000..a0babc888d3c
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -0,0 +1,188 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_PLUGINSPLIT"
+    script "../main.nf"
+    process "BCFTOOLS_PLUGINSPLIT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/pluginsplit"
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub") {
+
+        config "./nextflow.config"
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
new file mode 100644
index 000000000000..7b3635d5297b
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -0,0 +1,356 @@
+{
+    "homo_sapiens - [\u00a0vcf, tbi ], [], groups, regions, targets -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:36:55.844388572"
+    },
+    "homo_sapiens - [\u00a0vcf, tbi ], [], groups, regions, targets": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,78e962c3a724790b27041f28a4180600",
+                            "tumour.vcf:md5,3008a0a06a2f319897fa04ea0018fcdd"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,78e962c3a724790b27041f28a4180600",
+                            "tumour.vcf:md5,3008a0a06a2f319897fa04ea0018fcdd"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:08:37.030370035"
+    },
+    "homo_sapiens - [\u00a0vcf, tbi ], [], groups, regions, targets - tbi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf.gz:md5,78e962c3a724790b27041f28a4180600",
+                            "tumour.vcf.gz:md5,3008a0a06a2f319897fa04ea0018fcdd"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d",
+                            "tumour.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d"
+                        ]
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d",
+                            "tumour.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d"
+                        ]
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf.gz:md5,78e962c3a724790b27041f28a4180600",
+                            "tumour.vcf.gz:md5,3008a0a06a2f319897fa04ea0018fcdd"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:24:20.208432623"
+    },
+    "homo_sapiens - [\u00a0vcf, tbi ], [], groups, regions, targets - tbi -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "40001.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "40001.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:47:56.373929032"
+    },
+    "homo_sapiens - [\u00a0vcf, tbi ], samples, [], [], [] -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "tumour.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "tumour.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:35:44.991061535"
+    },
+    "homo_sapiens - [\u00a0vcf, tbi ], samples, [], [], []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,69cfc4bf92bf3e2847081a2026a4d3bb",
+                            "tumour.vcf:md5,08fa5c8d5561c2a8d7c300cb0eea1042"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,69cfc4bf92bf3e2847081a2026a4d3bb",
+                            "tumour.vcf:md5,08fa5c8d5561c2a8d7c300cb0eea1042"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:01:29.10055348"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/nextflow.config b/modules/nf-core/bcftools/pluginsplit/tests/nextflow.config
new file mode 100644
index 000000000000..9b9a4783a577
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'BCFTOOLS_PLUGINSPLIT' {
+        ext.args = '--write-index=tbi --output-type z'
+    }
+}
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/tags.yml b/modules/nf-core/bcftools/pluginsplit/tests/tags.yml
new file mode 100644
index 000000000000..2f29ef18ac8f
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/pluginsplit:
+  - "modules/nf-core/bcftools/pluginsplit/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 3672a771f065..92a100680f9d 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -103,9 +103,6 @@ bcftools/convert:
 bcftools/merge:
   - modules/nf-core/bcftools/merge/**
   - tests/modules/nf-core/bcftools/merge/**
-bcftools/pluginsplit:
-  - modules/nf-core/bcftools/pluginsplit/**
-  - tests/modules/nf-core/bcftools/pluginsplit/**
 bcftools/roh:
   - modules/nf-core/bcftools/roh/**
   - tests/modules/nf-core/bcftools/roh/**
diff --git a/tests/modules/nf-core/bcftools/pluginsplit/main.nf b/tests/modules/nf-core/bcftools/pluginsplit/main.nf
deleted file mode 100644
index abc615788d5e..000000000000
--- a/tests/modules/nf-core/bcftools/pluginsplit/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_PLUGINSPLIT } from '../../../../../modules/nf-core/bcftools/pluginsplit/main.nf'
-
-workflow test_bcftools_pluginsplit {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    samples = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
-        .collectFile(name:"samples.txt", newLine:true)
-
-    BCFTOOLS_PLUGINSPLIT (
-        input,
-        samples,
-        [],
-        [],
-        []
-    )
-}
-
-workflow test_bcftools_pluginsplit_full {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    groups = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
-        .collectFile(name:"samples.txt", newLine:true)
-
-    regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    targets = file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
-
-    BCFTOOLS_PLUGINSPLIT (
-        input,
-        [],
-        groups,
-        regions,
-        targets
-    )
-}
diff --git a/tests/modules/nf-core/bcftools/pluginsplit/nextflow.config b/tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bcftools/pluginsplit/test.yml b/tests/modules/nf-core/bcftools/pluginsplit/test.yml
deleted file mode 100644
index 48ecbfbff863..000000000000
--- a/tests/modules/nf-core/bcftools/pluginsplit/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: bcftools pluginsplit test_bcftools_pluginsplit
-  command: nextflow run ./tests/modules/nf-core/bcftools/pluginsplit -entry test_bcftools_pluginsplit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/pluginsplit
-  files:
-    - path: output/bcftools/normal.vcf
-      md5sum: 69cfc4bf92bf3e2847081a2026a4d3bb
-    - path: output/bcftools/tumour.vcf
-      md5sum: 08fa5c8d5561c2a8d7c300cb0eea1042
-    - path: output/bcftools/versions.yml
-
-- name: bcftools pluginsplit test_bcftools_pluginsplit_full
-  command: nextflow run ./tests/modules/nf-core/bcftools/pluginsplit -entry test_bcftools_pluginsplit_full -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/pluginsplit
-  files:
-    - path: output/bcftools/normal.vcf
-      md5sum: 78e962c3a724790b27041f28a4180600
-    - path: output/bcftools/tumour.vcf
-      md5sum: 3008a0a06a2f319897fa04ea0018fcdd
-    - path: output/bcftools/versions.yml