From 44e975ae83ca76a0f399b0c4bdce5ac0ef0d5eaf Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 10:26:25 +0100
Subject: [PATCH 01/13] update bcftools pluginsplit

---
 modules/nf-core/bcftools/pluginsplit/main.nf  |  48 +++-
 .../bcftools/pluginsplit/tests/main.nf.test   |  68 +++++-
 .../pluginsplit/tests/main.nf.test.snap       | 231 ++++++++++++++++--
 .../pluginsplit/tests/nextflow_suffix.config  |   6 +
 4 files changed, 322 insertions(+), 31 deletions(-)
 create mode 100644 modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 082802be709..24a374be4bf 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -15,10 +15,10 @@ process BCFTOOLS_PLUGINSPLIT {
     path(targets)
 
     output:
-    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
+    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
@@ -26,6 +26,7 @@ process BCFTOOLS_PLUGINSPLIT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: ""
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -42,7 +43,17 @@ process BCFTOOLS_PLUGINSPLIT {
         ${targets_arg} \\
         --output ${prefix}
 
-    mv ${prefix}/* .
+    for file in ${prefix}/*; do
+        # Extract the basename
+        base_name=\$(basename "\$file")
+        # Extract the part of the basename before the first dot
+        name_before_dot="\${base_name%%.*}"
+        # Extract the extension
+        extension="\${base_name#\${name_before_dot}}"
+        # Construct the new name
+        new_name="\${name_before_dot}${suffix}\${extension}"
+        mv "\$file" "${prefix}/\$new_name"
+    done
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -53,6 +64,7 @@ process BCFTOOLS_PLUGINSPLIT {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.suffix ?: ""
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -65,11 +77,29 @@ process BCFTOOLS_PLUGINSPLIT {
                 ""
     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)" : ""
     """
-    ${create_files}
-    ${create_index}
+    mkdir -p ${prefix}
+
+    cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
+    while IFS= read -r filename;
+    do ${create_cmd} "${prefix}/\$filename";
+    if [ -n "${index}" ]; then
+        index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
+        touch ${prefix}/\$index_file;
+    fi;
+    done < files.txt
+
+    for file in ${prefix}/*; do
+        # Extract the basename
+        base_name=\$(basename "\$file")
+        # Extract the part of the basename before the first dot
+        name_before_dot="\${base_name%%.*}"
+        # Extract the extension
+        extension="\${base_name#\${name_before_dot}}"
+        # Construct the new name
+        new_name="\${name_before_dot}${suffix}\${extension}"
+        mv "\$file" "${prefix}/\$new_name"
+    done
 
     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
index e3160851893..786c545cd4b 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -90,17 +90,42 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.vcf,
-                    process.out.tbi.get(0).get(1).find { file(it).name.matches("normal.vcf.gz.tbi|tumor.vcf.gz.tbi") },
-                ) }
+                { assert snapshot(process.out).match() }
             )
         }
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix") {
 
+        config "./nextflow_suffix.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
         options "-stub"
 
         when {
@@ -130,7 +155,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub") {
-
         options "-stub"
 
         when {
@@ -160,7 +184,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub") {
-
         config "./nextflow.config"
         options "-stub"
 
@@ -189,4 +212,35 @@ nextflow_process {
         }
 
     }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix -stub") {
+
+        config "./nextflow_suffix.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] = 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() }
+            )
+        }
+
+    }
 }
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index 66c3c1dda5e..f5fe024b2a5 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -1,4 +1,75 @@
 {
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "tumour.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "tumour.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "tumour.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "tumour.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-18T10:22:56.93123902"
+    },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub": {
         "content": [
             {
@@ -47,18 +118,148 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-09T15:56:42.307673651"
+        "timestamp": "2024-11-18T10:14:37.188961484"
+    },
+    "homo_sapiens - [ vcf, 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": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-18T10:21:51.332969425"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
         "content": null,
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-18T10:13:57.286300359"
+    },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-09T15:56:21.498991402"
+        "timestamp": "2024-11-18T10:22:03.743478849"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": {
         "content": [
@@ -126,10 +327,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-09T15:57:04.483688966"
+        "timestamp": "2024-11-18T10:15:04.70664725"
     },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], []": {
         "content": [
@@ -179,10 +380,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-09T15:56:10.033818589"
+        "timestamp": "2024-11-18T10:13:43.126600204"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": {
         "content": [
@@ -232,9 +433,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-09T15:56:53.641165787"
+        "timestamp": "2024-11-18T10:14:51.588072251"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config
new file mode 100644
index 00000000000..97aeb549f6b
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config
@@ -0,0 +1,6 @@
+process {
+    withName: 'BCFTOOLS_PLUGINSPLIT' {
+        ext.suffix = ".suffix"
+        ext.args = '--write-index=tbi --output-type z'
+    }
+}

From 13b4f2b775a6851909bd432819e347ff6acced1a Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 11:03:37 +0100
Subject: [PATCH 02/13] Add error test

---
 modules/nf-core/bcftools/pluginsplit/main.nf  | 48 ++++++++++---------
 modules/nf-core/bcftools/pluginsplit/meta.yml |  6 +--
 .../bcftools/pluginsplit/tests/main.nf.test   | 32 ++++++++++++-
 3 files changed, 60 insertions(+), 26 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 24a374be4bf..92b54ee96f2 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -43,17 +43,19 @@ process BCFTOOLS_PLUGINSPLIT {
         ${targets_arg} \\
         --output ${prefix}
 
-    for file in ${prefix}/*; do
-        # Extract the basename
-        base_name=\$(basename "\$file")
-        # Extract the part of the basename before the first dot
-        name_before_dot="\${base_name%%.*}"
-        # Extract the extension
-        extension="\${base_name#\${name_before_dot}}"
-        # Construct the new name
-        new_name="\${name_before_dot}${suffix}\${extension}"
-        mv "\$file" "${prefix}/\$new_name"
-    done
+    if [ -n "${suffix}" ]; then
+        for file in ${prefix}/*; do
+            # Extract the basename
+            base_name=\$(basename "\$file")
+            # Extract the part of the basename before the first dot
+            name_before_dot="\${base_name%%.*}"
+            # Extract the extension
+            extension="\${base_name#\${name_before_dot}}"
+            # Construct the new name
+            new_name="\${name_before_dot}${suffix}\${extension}"
+            mv "\$file" "${prefix}/\$new_name"
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -89,17 +91,19 @@ process BCFTOOLS_PLUGINSPLIT {
     fi;
     done < files.txt
 
-    for file in ${prefix}/*; do
-        # Extract the basename
-        base_name=\$(basename "\$file")
-        # Extract the part of the basename before the first dot
-        name_before_dot="\${base_name%%.*}"
-        # Extract the extension
-        extension="\${base_name#\${name_before_dot}}"
-        # Construct the new name
-        new_name="\${name_before_dot}${suffix}\${extension}"
-        mv "\$file" "${prefix}/\$new_name"
-    done
+    if [ -n "${suffix}" ]; then
+        for file in ${prefix}/*; do
+            # Extract the basename
+            base_name=\$(basename "\$file")
+            # Extract the part of the basename before the first dot
+            name_before_dot="\${base_name%%.*}"
+            # Extract the extension
+            extension="\${base_name#\${name_before_dot}}"
+            # Construct the new name
+            new_name="\${name_before_dot}${suffix}\${extension}"
+            mv "\$file" "${prefix}/\$new_name"
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml
index 41f766584fb..0c548858c5c 100644
--- a/modules/nf-core/bcftools/pluginsplit/meta.yml
+++ b/modules/nf-core/bcftools/pluginsplit/meta.yml
@@ -61,7 +61,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
+      - "/*.{vcf,vcf.gz,bcf,bcf.gz}":
           type: file
           description: The resulting VCF files from the split
           pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
@@ -71,7 +71,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.tbi":
+      - "/*.tbi":
           type: file
           description: TBI file
           pattern: "*.tbi"
@@ -81,7 +81,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.csi":
+      - "/*.csi":
           type: file
           description: CSI file
           pattern: "*.csi"
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index 786c545cd4b..baf9bb203f4 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -96,7 +96,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix") {
+    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with suffix") {
 
         config "./nextflow_suffix.config"
 
@@ -125,6 +125,36 @@ nextflow_process {
 
     }
 
+    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
+        tag "test"
+
+        config "./nextflow_suffix.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz") }
+            )
+        }
+
+    }
+
     test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
         options "-stub"
 

From 3a0ffd90f8e52dcd71bf8a190831a9c8ccc6a516 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 11:38:37 +0100
Subject: [PATCH 03/13] Fix test and meta

---
 modules/nf-core/bcftools/pluginsplit/meta.yml          |  6 +++---
 .../nf-core/bcftools/pluginsplit/tests/main.nf.test    |  1 -
 .../bcftools/pluginsplit/tests/main.nf.test.snap       | 10 +++++-----
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml
index 0c548858c5c..e9f6a6c4731 100644
--- a/modules/nf-core/bcftools/pluginsplit/meta.yml
+++ b/modules/nf-core/bcftools/pluginsplit/meta.yml
@@ -61,7 +61,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "/*.{vcf,vcf.gz,bcf,bcf.gz}":
+      - "*/*.{vcf,vcf.gz,bcf,bcf.gz}":
           type: file
           description: The resulting VCF files from the split
           pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
@@ -71,7 +71,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "/*.tbi":
+      - "*/*.tbi":
           type: file
           description: TBI file
           pattern: "*.tbi"
@@ -81,7 +81,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "/*.csi":
+      - "*/*.csi":
           type: file
           description: CSI file
           pattern: "*.csi"
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index baf9bb203f4..95987c4e24f 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -126,7 +126,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
-        tag "test"
 
         config "./nextflow_suffix.config"
 
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index f5fe024b2a5..825f4815e2d 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -145,8 +145,8 @@
                             "single_end": false
                         },
                         [
-                            "normal.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d",
-                            "tumour.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d"
+                            "normal.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905",
+                            "tumour.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
                         ]
                     ]
                 ],
@@ -166,8 +166,8 @@
                             "single_end": false
                         },
                         [
-                            "normal.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d",
-                            "tumour.vcf.gz.tbi:md5,e7180bb953d2bd657c420a5f76a7164d"
+                            "normal.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905",
+                            "tumour.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
                         ]
                     ]
                 ],
@@ -192,7 +192,7 @@
             "nf-test": "0.9.1",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-18T10:21:51.332969425"
+        "timestamp": "2024-11-18T11:34:33.850283173"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
         "content": null,

From e0fca182d9b38b2b110b3b70ef2d8ebb019a2292 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 12:30:54 +0100
Subject: [PATCH 04/13] Fix test

---
 .../bcftools/pluginsplit/tests/main.nf.test   |  5 +-
 .../pluginsplit/tests/main.nf.test.snap       | 74 +++----------------
 2 files changed, 16 insertions(+), 63 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index 95987c4e24f..e46ef43c774 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -90,7 +90,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.vcf.collect{ it[1].collect { file(it).name } },
+                    process.out.tbi.collect{ it[1].collect { file(it).name } },
+                ).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
index 825f4815e2d..6f05bbe8a76 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -125,74 +125,24 @@
     },
     "homo_sapiens - [ vcf, 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:md5,4cb176febbc8c26d717a6c6e67b9c905",
-                            "tumour.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
-                        ]
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ],
-                "csi": [
-                    
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "normal.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905",
-                            "tumour.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
-                        ]
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "normal.vcf.gz:md5,78e962c3a724790b27041f28a4180600",
-                            "tumour.vcf.gz:md5,3008a0a06a2f319897fa04ea0018fcdd"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+            [
+                [
+                    "normal.vcf.gz",
+                    "tumour.vcf.gz"
                 ]
-            }
+            ],
+            [
+                [
+                    "normal.vcf.gz.tbi",
+                    "tumour.vcf.gz.tbi"
+                ]
+            ]
         ],
         "meta": {
             "nf-test": "0.9.1",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-18T11:34:33.850283173"
+        "timestamp": "2024-11-18T12:29:33.856016049"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
         "content": null,

From b1e171bbfdda8cd37f8ebcae963aaf3c0cdccb21 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 13:23:19 +0100
Subject: [PATCH 05/13] Change extension detection

---
 modules/nf-core/bcftools/pluginsplit/main.nf  | 22 ++++---
 .../bcftools/pluginsplit/tests/main.nf.test   |  1 -
 .../pluginsplit/tests/main.nf.test.snap       | 59 +++++++++++++++++++
 3 files changed, 73 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 92b54ee96f2..896e9a74359 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -47,12 +47,15 @@ process BCFTOOLS_PLUGINSPLIT {
         for file in ${prefix}/*; do
             # Extract the basename
             base_name=\$(basename "\$file")
-            # Extract the part of the basename before the first dot
-            name_before_dot="\${base_name%%.*}"
             # Extract the extension
-            extension="\${base_name#\${name_before_dot}}"
+            extension=""
+            # Remove the extension if it exists
+            if [[ "\$base_name" =~ \\.(vcf|bcf)(\\.gz)?(\\.tbi|\\.csi)?\$ ]]; then
+                extension="\${BASH_REMATCH[0]}"
+                base_name="\${base_name%\$extension}"
+            fi
             # Construct the new name
-            new_name="\${name_before_dot}${suffix}\${extension}"
+            new_name="\${base_name}${suffix}\${extension}"
             mv "\$file" "${prefix}/\$new_name"
         done
     fi
@@ -95,12 +98,15 @@ process BCFTOOLS_PLUGINSPLIT {
         for file in ${prefix}/*; do
             # Extract the basename
             base_name=\$(basename "\$file")
-            # Extract the part of the basename before the first dot
-            name_before_dot="\${base_name%%.*}"
             # Extract the extension
-            extension="\${base_name#\${name_before_dot}}"
+            extension=""
+            # Remove the extension if it exists
+            if [[ "\$base_name" =~ \\.(vcf|bcf)(\\.gz)?(\\.tbi|\\.csi)?\$ ]]; then
+                extension="\${BASH_REMATCH[0]}"
+                base_name="\${base_name%\$extension}"
+            fi
             # Construct the new name
-            new_name="\${name_before_dot}${suffix}\${extension}"
+            new_name="\${base_name}${suffix}\${extension}"
             mv "\$file" "${prefix}/\$new_name"
         done
     fi
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index e46ef43c774..6e201770614 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -100,7 +100,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with suffix") {
-
         config "./nextflow_suffix.config"
 
         when {
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index 6f05bbe8a76..afcfadd5879 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -1,4 +1,63 @@
 {
+    "homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with suffix": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-18T13:20:35.912534311"
+    },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix -stub": {
         "content": [
             {

From b790fe99d4b92581957eca9ba29fdd9d78f1ac86 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 14:31:42 +0100
Subject: [PATCH 06/13] Change file renaming

---
 modules/nf-core/bcftools/pluginsplit/main.nf  | 48 +++++--------------
 .../bcftools/pluginsplit/tests/main.nf.test   |  8 ++--
 ...w_suffix.config => nextflow_prefix.config} |  1 +
 3 files changed, 17 insertions(+), 40 deletions(-)
 rename modules/nf-core/bcftools/pluginsplit/tests/{nextflow_suffix.config => nextflow_prefix.config} (80%)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 896e9a74359..c38d414b1c8 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -25,8 +25,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: ""
+    def prefix = task.ext.prefix ?: ""
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -41,22 +40,11 @@ process BCFTOOLS_PLUGINSPLIT {
         ${groups_arg} \\
         ${regions_arg} \\
         ${targets_arg} \\
-        --output ${prefix}
+        --output outputDir
 
-    if [ -n "${suffix}" ]; then
-        for file in ${prefix}/*; do
-            # Extract the basename
-            base_name=\$(basename "\$file")
-            # Extract the extension
-            extension=""
-            # Remove the extension if it exists
-            if [[ "\$base_name" =~ \\.(vcf|bcf)(\\.gz)?(\\.tbi|\\.csi)?\$ ]]; then
-                extension="\${BASH_REMATCH[0]}"
-                base_name="\${base_name%\$extension}"
-            fi
-            # Construct the new name
-            new_name="\${base_name}${suffix}\${extension}"
-            mv "\$file" "${prefix}/\$new_name"
+    if [ -n "${prefix}" ]; then
+        for file in outputDir/*; do
+            mv \$file outputDir/${prefix}\$file
         done
     fi
 
@@ -68,8 +56,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: ""
+    def prefix = task.ext.prefix ?: ""
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -83,31 +70,20 @@ process BCFTOOLS_PLUGINSPLIT {
     def determination_file = samples ?: targets
     def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
     """
-    mkdir -p ${prefix}
+    mkdir -p outputDir
 
     cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
     while IFS= read -r filename;
-    do ${create_cmd} "${prefix}/\$filename";
+    do ${create_cmd} "outputDir/\$filename";
     if [ -n "${index}" ]; then
         index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
-        touch ${prefix}/\$index_file;
+        touch outputDir/\$index_file;
     fi;
     done < files.txt
 
-    if [ -n "${suffix}" ]; then
-        for file in ${prefix}/*; do
-            # Extract the basename
-            base_name=\$(basename "\$file")
-            # Extract the extension
-            extension=""
-            # Remove the extension if it exists
-            if [[ "\$base_name" =~ \\.(vcf|bcf)(\\.gz)?(\\.tbi|\\.csi)?\$ ]]; then
-                extension="\${BASH_REMATCH[0]}"
-                base_name="\${base_name%\$extension}"
-            fi
-            # Construct the new name
-            new_name="\${base_name}${suffix}\${extension}"
-            mv "\$file" "${prefix}/\$new_name"
+    if [ -n "${prefix}" ]; then
+        for file in outputDir/*; do
+            mv \$file outputDir/${prefix}\$file
         done
     fi
 
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index 6e201770614..9aba68a8120 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -99,8 +99,8 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with suffix") {
-        config "./nextflow_suffix.config"
+    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix") {
+        config "./nextflow_prefix.config"
 
         when {
             process {
@@ -244,9 +244,9 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix -stub") {
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub") {
 
-        config "./nextflow_suffix.config"
+        config "./nextflow_prefix.config"
         options "-stub"
 
         when {
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
similarity index 80%
rename from modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config
rename to modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
index 97aeb549f6b..9678fdef44f 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_suffix.config
+++ b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
@@ -1,5 +1,6 @@
 process {
     withName: 'BCFTOOLS_PLUGINSPLIT' {
+        ext.prefix = "${meta.id}."
         ext.suffix = ".suffix"
         ext.args = '--write-index=tbi --output-type z'
     }

From 4e25cd60a27574026815dbaf9c614220ad09c44d Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 16:09:01 +0100
Subject: [PATCH 07/13] Fix renaming

---
 modules/nf-core/bcftools/pluginsplit/main.nf  |   4 +-
 .../bcftools/pluginsplit/tests/main.nf.test   |   4 +-
 .../pluginsplit/tests/main.nf.test.snap       | 130 ++++++++++++++++++
 .../pluginsplit/tests/nextflow_prefix.config  |   3 +-
 4 files changed, 136 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index c38d414b1c8..cc15c298171 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -44,7 +44,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     if [ -n "${prefix}" ]; then
         for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\$file
+            mv \$file outputDir/${prefix}\${file##*/}
         done
     fi
 
@@ -83,7 +83,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     if [ -n "${prefix}" ]; then
         for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\$file
+            mv \$file outputDir/${prefix}\${file##*/}
         done
     fi
 
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index 9aba68a8120..009897b6393 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -100,6 +100,7 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix") {
+
         config "./nextflow_prefix.config"
 
         when {
@@ -129,7 +130,7 @@ nextflow_process {
 
     test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
 
-        config "./nextflow_suffix.config"
+        config "./nextflow_prefix.config"
 
         when {
             process {
@@ -246,6 +247,7 @@ nextflow_process {
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub") {
 
+        tag "test"
         config "./nextflow_prefix.config"
         options "-stub"
 
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index afcfadd5879..56728077a36 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -58,6 +58,77 @@
         },
         "timestamp": "2024-11-18T13:20:35.912534311"
     },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_normal.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_tumour.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_normal.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_tumour.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_normal.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_tumour.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_normal.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_tumour.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-18T16:08:02.684907361"
+    },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix -stub": {
         "content": [
             {
@@ -129,6 +200,65 @@
         },
         "timestamp": "2024-11-18T10:22:56.93123902"
     },
+    "homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_NA24385.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_NA24385.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_NA24385.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_NA24385.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-18T15:21:56.957577603"
+    },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub": {
         "content": [
             {
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
index 9678fdef44f..9715a649291 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
+++ b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
@@ -1,7 +1,6 @@
 process {
     withName: 'BCFTOOLS_PLUGINSPLIT' {
-        ext.prefix = "${meta.id}."
-        ext.suffix = ".suffix"
+        ext.prefix = {"${meta.id}_"} // Add a prefix to the output files
         ext.args = '--write-index=tbi --output-type z'
     }
 }

From 8e7eb1760022041a04283fc1cc8a9285a72cdbcf Mon Sep 17 00:00:00 2001
From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Date: Mon, 18 Nov 2024 16:31:55 +0100
Subject: [PATCH 08/13] Update modules/nf-core/bcftools/pluginsplit/main.nf

Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com>
---
 modules/nf-core/bcftools/pluginsplit/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index cc15c298171..0a757e6b2be 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -15,9 +15,9 @@ process BCFTOOLS_PLUGINSPLIT {
     path(targets)
 
     output:
-    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
+    tuple val(meta), path("outputDir/*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("outputDir/*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("outputDir/*.csi")                    , emit: csi, optional: true
     path "versions.yml"                                 , emit: versions
 
     when:

From ee7edb5d6fd59f544aa756a2ccf83b65134e7dda Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gamil.com>
Date: Mon, 18 Nov 2024 16:40:45 +0100
Subject: [PATCH 09/13] Update bcftools pluginsplit

---
 modules/nf-core/bcftools/pluginsplit/main.nf  |  12 +-
 modules/nf-core/bcftools/pluginsplit/meta.yml |   6 +-
 .../pluginsplit/tests/main.nf.test.snap       | 227 ++----------------
 3 files changed, 29 insertions(+), 216 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 0a757e6b2be..df4145fe355 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -25,6 +25,8 @@ process BCFTOOLS_PLUGINSPLIT {
 
     script:
     def args = task.ext.args ?: ''
+    // Here the default prefix is an empty string as the filename is created by the plugin
+    // and the prefix is instead added to the output files in the script
     def prefix = task.ext.prefix ?: ""
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
@@ -74,11 +76,11 @@ process BCFTOOLS_PLUGINSPLIT {
 
     cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
     while IFS= read -r filename;
-    do ${create_cmd} "outputDir/\$filename";
-    if [ -n "${index}" ]; then
-        index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
-        touch outputDir/\$index_file;
-    fi;
+        do ${create_cmd} "outputDir/\$filename";
+        if [ -n "${index}" ]; then
+            index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
+            touch outputDir/\$index_file;
+        fi;
     done < files.txt
 
     if [ -n "${prefix}" ]; then
diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml
index e9f6a6c4731..7fbc7d411eb 100644
--- a/modules/nf-core/bcftools/pluginsplit/meta.yml
+++ b/modules/nf-core/bcftools/pluginsplit/meta.yml
@@ -61,7 +61,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*/*.{vcf,vcf.gz,bcf,bcf.gz}":
+      - "outputDir/*.{vcf,vcf.gz,bcf,bcf.gz}":
           type: file
           description: The resulting VCF files from the split
           pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
@@ -71,7 +71,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*/*.tbi":
+      - "outputDir/*.tbi":
           type: file
           description: TBI file
           pattern: "*.tbi"
@@ -81,7 +81,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*/*.csi":
+      - "outputDir/*.csi":
           type: file
           description: CSI file
           pattern: "*.csi"
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index 56728077a36..64f55df7b01 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -1,63 +1,4 @@
 {
-    "homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with suffix": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ],
-                "csi": [
-                    
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-18T13:20:35.912534311"
-    },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub": {
         "content": [
             {
@@ -86,13 +27,13 @@
                     ]
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-                    
+
                 ],
                 "tbi": [
                     [
@@ -129,77 +70,6 @@
         },
         "timestamp": "2024-11-18T16:08:02.684907361"
     },
-    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix -stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "normal.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "tumour.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "normal.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "tumour.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ],
-                "csi": [
-                    
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "normal.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "tumour.suffix.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "normal.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "tumour.suffix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-18T10:22:56.93123902"
-    },
     "homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix": {
         "content": [
             {
@@ -222,13 +92,13 @@
                     ]
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-                    
+
                 ],
                 "tbi": [
                     [
@@ -275,19 +145,19 @@
                     ]
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-                    
+
                 ],
                 "tbi": [
-                    
+
                 ],
                 "vcf": [
                     [
@@ -341,65 +211,6 @@
         },
         "timestamp": "2024-11-18T10:13:57.286300359"
     },
-    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with suffix": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
-                    ]
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ],
-                "csi": [
-                    
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "NA24385.suffix.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-18T10:22:03.743478849"
-    },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": {
         "content": [
             {
@@ -428,13 +239,13 @@
                     ]
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-                    
+
                 ],
                 "tbi": [
                     [
@@ -487,19 +298,19 @@
                     ]
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-                    
+
                 ],
                 "tbi": [
-                    
+
                 ],
                 "vcf": [
                     [
@@ -540,19 +351,19 @@
                     ]
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-                    
+
                 ],
                 "tbi": [
-                    
+
                 ],
                 "vcf": [
                     [
@@ -577,4 +388,4 @@
         },
         "timestamp": "2024-11-18T10:14:51.588072251"
     }
-}
\ No newline at end of file
+}

From 8e9cde653ecf4064a77f9856df649bf03212c748 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 20 Nov 2024 15:02:49 +0100
Subject: [PATCH 10/13] Stage input in folder

---
 modules/nf-core/bcftools/pluginsplit/main.nf  |  34 +--
 .../bcftools/pluginsplit/tests/main.nf.test   |  67 +-----
 .../pluginsplit/tests/main.nf.test.snap       | 196 +++---------------
 .../pluginsplit/tests/nextflow_prefix.config  |   6 -
 4 files changed, 43 insertions(+), 260 deletions(-)
 delete mode 100644 modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index df4145fe355..1ab7943f9e4 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -8,26 +8,23 @@ process BCFTOOLS_PLUGINSPLIT {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta), path(vcf, stageAs: "?/*"), path(tbi, stageAs: "?/*")
     path(samples)
     path(groups)
     path(regions)
     path(targets)
 
     output:
-    tuple val(meta), path("outputDir/*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
-    tuple val(meta), path("outputDir/*.tbi")                    , emit: tbi, optional: true
-    tuple val(meta), path("outputDir/*.csi")                    , emit: csi, optional: true
-    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
 
     script:
     def args = task.ext.args ?: ''
-    // Here the default prefix is an empty string as the filename is created by the plugin
-    // and the prefix is instead added to the output files in the script
-    def prefix = task.ext.prefix ?: ""
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -42,13 +39,7 @@ process BCFTOOLS_PLUGINSPLIT {
         ${groups_arg} \\
         ${regions_arg} \\
         ${targets_arg} \\
-        --output outputDir
-
-    if [ -n "${prefix}" ]; then
-        for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\${file##*/}
-        done
-    fi
+        --output .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -58,7 +49,6 @@ process BCFTOOLS_PLUGINSPLIT {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: ""
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -72,23 +62,15 @@ process BCFTOOLS_PLUGINSPLIT {
     def determination_file = samples ?: targets
     def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
     """
-    mkdir -p outputDir
-
     cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
     while IFS= read -r filename;
-        do ${create_cmd} "outputDir/\$filename";
+        do ${create_cmd} "./\$filename";
         if [ -n "${index}" ]; then
             index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
-            touch outputDir/\$index_file;
+            touch ./\$index_file;
         fi;
     done < files.txt
 
-    if [ -n "${prefix}" ]; then
-        for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\${file##*/}
-        done
-    fi
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index 009897b6393..c1d93453923 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -67,7 +67,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi") {
-
         config "./nextflow.config"
 
         when {
@@ -99,38 +98,8 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix") {
-
-        config "./nextflow_prefix.config"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi', checkIfExists: true)
-                ]
-                input[1] = []
-                input[2] = []
-                input[3] = []
-                input[4] = []
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
     test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
-
-        config "./nextflow_prefix.config"
+        config "./nextflow.config"
 
         when {
             process {
@@ -151,7 +120,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.failed },
-                { assert process.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz") }
+                { assert process.errorReport.contains("No samples to split: 1/dbsnp_146.hg38.vcf.gz") }
             )
         }
 
@@ -244,36 +213,4 @@ nextflow_process {
         }
 
     }
-
-    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub") {
-
-        tag "test"
-        config "./nextflow_prefix.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] = 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() }
-            )
-        }
-
-    }
 }
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
index 64f55df7b01..b915b7cf24f 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -1,134 +1,4 @@
 {
-    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi with prefix -stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test_normal.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_tumour.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test_normal.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test_tumour.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "2": [
-
-                ],
-                "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ],
-                "csi": [
-
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test_normal.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            "test_tumour.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                        ]
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test_normal.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_tumour.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-18T16:08:02.684907361"
-    },
-    "homo_sapiens - [ vcf, tbi ], [], [], [], [], - tbi with prefix": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_NA24385.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_NA24385.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
-                    ]
-                ],
-                "2": [
-
-                ],
-                "3": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ],
-                "csi": [
-
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_NA24385.vcf.gz.tbi:md5,7848669b7da31c6a5f680c0b4f4857d2"
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test_NA24385.vcf.gz:md5,a35bd27152b5a9bd9ce5bb3127c68693"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
-        },
-        "timestamp": "2024-11-18T15:21:56.957577603"
-    },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub": {
         "content": [
             {
@@ -145,19 +15,19 @@
                     ]
                 ],
                 "1": [
-
+                    
                 ],
                 "2": [
-
+                    
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-
+                    
                 ],
                 "tbi": [
-
+                    
                 ],
                 "vcf": [
                     [
@@ -177,10 +47,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T10:14:37.188961484"
+        "timestamp": "2024-11-20T14:56:54.383979416"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi": {
         "content": [
@@ -198,18 +68,18 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T12:29:33.856016049"
+        "timestamp": "2024-11-20T14:56:44.796391578"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
         "content": null,
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T10:13:57.286300359"
+        "timestamp": "2024-11-20T14:56:36.709842966"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": {
         "content": [
@@ -239,13 +109,13 @@
                     ]
                 ],
                 "2": [
-
+                    
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-
+                    
                 ],
                 "tbi": [
                     [
@@ -277,10 +147,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T10:15:04.70664725"
+        "timestamp": "2024-11-20T14:57:11.163588435"
     },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], []": {
         "content": [
@@ -298,19 +168,19 @@
                     ]
                 ],
                 "1": [
-
+                    
                 ],
                 "2": [
-
+                    
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-
+                    
                 ],
                 "tbi": [
-
+                    
                 ],
                 "vcf": [
                     [
@@ -330,10 +200,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T10:13:43.126600204"
+        "timestamp": "2024-11-20T14:56:27.978161766"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": {
         "content": [
@@ -351,19 +221,19 @@
                     ]
                 ],
                 "1": [
-
+                    
                 ],
                 "2": [
-
+                    
                 ],
                 "3": [
                     "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
                 ],
                 "csi": [
-
+                    
                 ],
                 "tbi": [
-
+                    
                 ],
                 "vcf": [
                     [
@@ -383,9 +253,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.0"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T10:14:51.588072251"
+        "timestamp": "2024-11-20T14:57:02.456908152"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config b/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
deleted file mode 100644
index 9715a649291..00000000000
--- a/modules/nf-core/bcftools/pluginsplit/tests/nextflow_prefix.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-    withName: 'BCFTOOLS_PLUGINSPLIT' {
-        ext.prefix = {"${meta.id}_"} // Add a prefix to the output files
-        ext.args = '--write-index=tbi --output-type z'
-    }
-}

From 2b5ca280c7ca3ac0aca32eca51a0c3f2fccf22d6 Mon Sep 17 00:00:00 2001
From: Louis <louislenezet@gmail.com>
Date: Wed, 20 Nov 2024 17:32:06 +0100
Subject: [PATCH 11/13] Fix meta.yml

---
 modules/nf-core/bcftools/pluginsplit/meta.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml
index 7fbc7d411eb..41f766584fb 100644
--- a/modules/nf-core/bcftools/pluginsplit/meta.yml
+++ b/modules/nf-core/bcftools/pluginsplit/meta.yml
@@ -61,7 +61,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "outputDir/*.{vcf,vcf.gz,bcf,bcf.gz}":
+      - "*.{vcf,vcf.gz,bcf,bcf.gz}":
           type: file
           description: The resulting VCF files from the split
           pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
@@ -71,7 +71,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "outputDir/*.tbi":
+      - "*.tbi":
           type: file
           description: TBI file
           pattern: "*.tbi"
@@ -81,7 +81,7 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "outputDir/*.csi":
+      - "*.csi":
           type: file
           description: CSI file
           pattern: "*.csi"

From c7b507af5bef14b4baef3df8e013331c5bf0b9a3 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 21 Nov 2024 11:38:17 +0100
Subject: [PATCH 12/13] Update input

---
 modules/nf-core/bcftools/pluginsplit/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 1ab7943f9e4..e541df114ed 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -8,7 +8,7 @@ process BCFTOOLS_PLUGINSPLIT {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf, stageAs: "?/*"), path(tbi, stageAs: "?/*")
+    tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*")
     path(samples)
     path(groups)
     path(regions)

From eb6154e279e8894c42e27e342e85374c5ca70f6a Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 21 Nov 2024 11:59:11 +0100
Subject: [PATCH 13/13] Update error report

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

diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
index c1d93453923..e7ae574e1b6 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -120,7 +120,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.failed },
-                { assert process.errorReport.contains("No samples to split: 1/dbsnp_146.hg38.vcf.gz") }
+                { assert process.errorReport.contains("No samples to split: input/dbsnp_146.hg38.vcf.gz") }
             )
         }