From a94009a5643b01f24069bf8cc89b9c3eaa35fef6 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Sun, 17 Nov 2024 19:17:01 +0100
Subject: [PATCH 01/17] Fix pluginsplit

---
 .../pluginsplit/bcftools-pluginsplit.diff         | 15 ++++++++++++++-
 modules/nf-core/bcftools/pluginsplit/main.nf      |  8 ++++----
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
index f06044e4..061e70e4 100644
--- a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
+++ b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
@@ -3,6 +3,19 @@ Changes in module 'nf-core/bcftools/pluginsplit'
 Changes in 'bcftools/pluginsplit/main.nf':
 --- modules/nf-core/bcftools/pluginsplit/main.nf
 +++ modules/nf-core/bcftools/pluginsplit/main.nf
+@@ -15,9 +15,9 @@
+     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("*/*.{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:
 @@ -26,11 +26,17 @@
      script:
      def args = task.ext.args ?: ''
@@ -35,7 +48,7 @@ Changes in 'bcftools/pluginsplit/main.nf':
 +        extension="\${base_name#\${name_before_dot}}"
 +        # Construct the new name
 +        new_name="\${name_before_dot}${suffix}\${extension}"
-+        mv "\$file" "./\$new_name"
++        mv "\$file" "${prefix}/\$new_name"
 +    done
  
      cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 8b493087..dce34f5f 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("*/*.{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:
@@ -57,7 +57,7 @@ process BCFTOOLS_PLUGINSPLIT {
         extension="\${base_name#\${name_before_dot}}"
         # Construct the new name
         new_name="\${name_before_dot}${suffix}\${extension}"
-        mv "\$file" "./\$new_name"
+        mv "\$file" "${prefix}/\$new_name"
     done
 
     cat <<-END_VERSIONS > versions.yml

From 4e0ce652ece03c8254cc076467bd24ceb6e70c05 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Sun, 17 Nov 2024 19:32:19 +0100
Subject: [PATCH 02/17] Update vcf_split_bcftools

---
 .../vcf_split_bcftools/tests/main.nf.test     | 58 +++++++++++++++++--
 .../tests/main.nf.test.snap                   | 29 ++++++++--
 .../vcf_split_bcftools/tests/nextflow.config  |  3 +
 3 files changed, 80 insertions(+), 10 deletions(-)

diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
index 46c09660..1864bb76 100644
--- a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
+++ b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_workflow {
     tag "bcftools"
     tag "bcftools/split"
 
-    test("Split vcf file") {
+    test("Split multiple vcf file") {
         setup {
             run("BCFTOOLS_MERGE") {
                 script "../../../../modules/nf-core/bcftools/merge/main.nf"
@@ -23,7 +23,7 @@ nextflow_workflow {
                 """
                 input[0] = Channel.of(
                     [
-                        [id: "allSamples"],
+                        [id: "allSamples.batch0"],
                         [file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf", checkIfExist:true),
                         file(params.pipelines_testdata_base_path + "hum_data/individuals/NA19401/NA19401.s_imputed.bcf", checkIfExist:true),
                         file(params.pipelines_testdata_base_path + "hum_data/individuals/NA20359/NA20359.s_imputed.bcf", checkIfExist:true)],
@@ -43,10 +43,6 @@ nextflow_workflow {
             }
         }
         when {
-            params {
-                max_cpus   = 2
-                max_memory = '2.GB'
-            }
             workflow {
                 """
                 input[0] = BCFTOOLS_MERGE.out.vcf.join(BCFTOOLS_MERGE.out.tbi)
@@ -74,4 +70,54 @@ nextflow_workflow {
             )
         }
     }
+
+    test("Split one sample vcf file") {
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [id: 'NA12878'],
+                    file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf", checkIfExist:true),
+                    file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf.csi", checkIfExist:true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.versions,
+                    workflow.out.vcf_tbi.collect{[
+                        it[0],
+                        path(it[1]).getFileName().toString(),
+                        path(it[2]).getFileName().toString()
+                    ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Split no sample vcf file") {
+        when {
+            workflow {
+                """
+                input[0] = Channel.of([
+                    [id: 'dbsnp_146.hg38'],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExist:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExist:true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.failed },
+                { assert workflow.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz")
+                }
+            )
+        }
+    }
 }
diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
index d3bd681e..02a8da3a 100644
--- a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
+++ b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
@@ -1,5 +1,26 @@
 {
-    "Split vcf file": {
+    "Split one sample vcf file": {
+        "content": [
+            [
+                "versions.yml:md5,6c3351d97e3a99f7a7a3231fc49f92e2"
+            ],
+            [
+                [
+                    {
+                        "id": "NA12878"
+                    },
+                    "NA12878.vcf.gz",
+                    "NA12878.vcf.gz.tbi"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-13T14:06:59.745818945"
+    },
+    "Split multiple vcf file": {
         "content": [
             [
                 "versions.yml:md5,6c3351d97e3a99f7a7a3231fc49f92e2"
@@ -34,9 +55,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.1",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-07T14:13:06.801872176"
+        "timestamp": "2024-11-11T14:42:48.076610625"
     }
-}
\ No newline at end of file
+}
diff --git a/subworkflows/local/vcf_split_bcftools/tests/nextflow.config b/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
index 523678dc..a2282fbf 100644
--- a/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
+++ b/subworkflows/local/vcf_split_bcftools/tests/nextflow.config
@@ -1,7 +1,10 @@
 process {
+    resourceLimits = [cpus: 2, memory: '2.GB']
+
     withName: BCFTOOLS_MERGE {
         ext.args = ["--write-index=tbi", "--output-type z"].join(' ')
     }
+
     withName: BCFTOOLS_PLUGINSPLIT {
         ext.args = ["--write-index=tbi", "--output-type z"].join(' ')
     }

From 04a12c2a5ac4f0d3ed33135203383ac5b767cbac Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 14:10:04 +0100
Subject: [PATCH 03/17] Fix config

---
 conf/modules.config                           |   3 +-
 .../pluginsplit/bcftools-pluginsplit.diff     | 100 +++++++++++++-----
 modules/nf-core/bcftools/pluginsplit/main.nf  |  68 ++++++++----
 3 files changed, 122 insertions(+), 49 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 693570cf..40c9af9e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -88,7 +88,8 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}_${meta.batch}" }
+        ext.prefix = { "${meta.id}.${meta.batch}" }
+        ext.suffix = { ".batch${meta.batch}.${meta.tools}" }
         publishDir = [
             path: { "${params.outdir}/imputation/${meta.tools}/samples/" },
             mode: params.publish_dir_mode,
diff --git a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
index 061e70e4..158c59af 100644
--- a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
+++ b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
@@ -3,20 +3,22 @@ Changes in module 'nf-core/bcftools/pluginsplit'
 Changes in 'bcftools/pluginsplit/main.nf':
 --- modules/nf-core/bcftools/pluginsplit/main.nf
 +++ modules/nf-core/bcftools/pluginsplit/main.nf
-@@ -15,9 +15,9 @@
+@@ -15,10 +15,10 @@
      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
++    path "versions.yml"                                 , emit: versions
  
      when:
-@@ -26,11 +26,17 @@
+     task.ext.when == null || task.ext.when
+@@ -26,6 +26,7 @@
      script:
      def args = task.ext.args ?: ''
      def prefix = task.ext.prefix ?: "${meta.id}"
@@ -24,36 +26,82 @@ Changes in 'bcftools/pluginsplit/main.nf':
  
      def samples_arg = samples ? "--samples-file ${samples}" : ""
      def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
-     def regions_arg = regions ? "--regions-file ${regions}" : ""
-     def targets_arg = targets ? "--targets-file ${targets}" : ""
-+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-+            args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-+            args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-+            args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-+            "vcf"
- 
-     """
-     bcftools plugin split \\
-@@ -42,7 +48,17 @@
+@@ -42,7 +43,22 @@
          ${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" "${prefix}/\$new_name"
-+    done
++    if [ -n "${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"
++        done
++    fi
  
      cat <<-END_VERSIONS > versions.yml
      "${task.process}":
-
+@@ -53,6 +69,7 @@
+     stub:
+     def args = task.ext.args ?: ''
+     def prefix = task.ext.prefix ?: "${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" :
+@@ -65,15 +82,38 @@
+                 ""
+     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 ${prefix}/\$index_file;
++    fi;
++    done < files.txt
++
++    if [ -n "${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" "${prefix}/\$new_name"
++        done
++    fi
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+     END_VERSIONS
+     """
+-}
++}
 'modules/nf-core/bcftools/pluginsplit/meta.yml' is unchanged
 'modules/nf-core/bcftools/pluginsplit/tests/main.nf.test' is unchanged
 'modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap' is unchanged
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index dce34f5f..0e0fb840 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -18,7 +18,7 @@ process BCFTOOLS_PLUGINSPLIT {
     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
+    path "versions.yml"                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,11 +32,6 @@ process BCFTOOLS_PLUGINSPLIT {
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
     def regions_arg = regions ? "--regions-file ${regions}" : ""
     def targets_arg = targets ? "--targets-file ${targets}" : ""
-    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
-            args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
-            args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
-            args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
-            "vcf"
 
     """
     bcftools plugin split \\
@@ -48,17 +43,22 @@ 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 ${prefix}/*; do
+            # Extract the basename
+            base_name=\$(basename "\$file")
+            # Extract the extension
+            extension=""
+            # Remove the extension if it exists
+            if [[ "\$base_name" =~ \\.(vcf|bcf)(\\.gz)?(\\.tbi|\\.csi)?\$ ]]; then
+                extension="\${BASH_REMATCH[0]}"
+                base_name="\${base_name%\$extension}"
+            fi
+            # Construct the new name
+            new_name="\${base_name}${suffix}\${extension}"
+            mv "\$file" "${prefix}/\$new_name"
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -69,6 +69,7 @@ process BCFTOOLS_PLUGINSPLIT {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${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" :
@@ -81,15 +82,38 @@ 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 ${prefix}/\$index_file;
+    fi;
+    done < files.txt
+
+    if [ -n "${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"
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
-}
+}
\ No newline at end of file

From 8c1fff6684786b269c9de71f917c90f1ccdf9c1f Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 17:44:03 +0100
Subject: [PATCH 04/17] Update pluginsplit

---
 conf/modules.config                           |   3 +-
 conf/steps/validation.config                  |   3 +-
 .../pluginsplit/bcftools-pluginsplit.diff     | 110 ------------------
 modules/nf-core/bcftools/pluginsplit/main.nf  |  64 ++++------
 nextflow.config                               |  48 ++++----
 5 files changed, 47 insertions(+), 181 deletions(-)
 delete mode 100644 modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff

diff --git a/conf/modules.config b/conf/modules.config
index 40c9af9e..2932d5f4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -88,8 +88,7 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}.${meta.batch}" }
-        ext.suffix = { ".batch${meta.batch}.${meta.tools}" }
+        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.tools}" }
         publishDir = [
             path: { "${params.outdir}/imputation/${meta.tools}/samples/" },
             mode: params.publish_dir_mode,
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index 10c7df52..285221d6 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -75,8 +75,7 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}" }
-        ext.suffix = ".truth"
+        ext.prefix = { "${meta.id}.truth" }
     }
 
     // Validation subworkflow
diff --git a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
deleted file mode 100644
index 158c59af..00000000
--- a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
+++ /dev/null
@@ -1,110 +0,0 @@
-Changes in module 'nf-core/bcftools/pluginsplit'
-'modules/nf-core/bcftools/pluginsplit/environment.yml' is unchanged
-Changes in 'bcftools/pluginsplit/main.nf':
---- modules/nf-core/bcftools/pluginsplit/main.nf
-+++ modules/nf-core/bcftools/pluginsplit/main.nf
-@@ -15,10 +15,10 @@
-     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 @@
-     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 +43,22 @@
-         ${targets_arg} \\
-         --output ${prefix}
- 
--    mv ${prefix}/* .
-+    if [ -n "${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" "${prefix}/\$new_name"
-+        done
-+    fi
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-@@ -53,6 +69,7 @@
-     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" :
-@@ -65,15 +82,38 @@
-                 ""
-     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 ${prefix}/\$index_file;
-+    fi;
-+    done < files.txt
-+
-+    if [ -n "${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" "${prefix}/\$new_name"
-+        done
-+    fi
- 
-     cat <<-END_VERSIONS > versions.yml
-     "${task.process}":
-         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
-     END_VERSIONS
-     """
--}
-+}
-'modules/nf-core/bcftools/pluginsplit/meta.yml' is unchanged
-'modules/nf-core/bcftools/pluginsplit/tests/main.nf.test' is unchanged
-'modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/bcftools/pluginsplit/tests/nextflow.config' is unchanged
-'modules/nf-core/bcftools/pluginsplit/tests/tags.yml' is unchanged
-************************************************************
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 0e0fb840..df4145fe 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:
@@ -25,8 +25,9 @@ process BCFTOOLS_PLUGINSPLIT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: ""
+    // 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}"   : ""
@@ -41,22 +42,11 @@ 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 +58,7 @@ 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 +72,20 @@ 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";
-    if [ -n "${index}" ]; then
-        index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
-        touch ${prefix}/\$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 "${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
 
@@ -116,4 +94,4 @@ process BCFTOOLS_PLUGINSPLIT {
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
-}
\ No newline at end of file
+}
diff --git a/nextflow.config b/nextflow.config
index 3e402c96..5fb08a09 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -103,6 +103,30 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
+// initialisation step
+includeConfig 'conf/steps/initialisation.config'
+
+// chrcheck workflow
+includeConfig 'conf/steps/chrcheck.config'
+
+// simulation step
+includeConfig 'conf/steps/simulation.config'
+
+// panel_prep step
+includeConfig 'conf/steps/panel_prep.config'
+
+// imputation step
+includeConfig 'conf/steps/imputation_glimpse1.config'
+includeConfig 'conf/steps/imputation_quilt.config'
+includeConfig 'conf/steps/imputation_stitch.config'
+includeConfig 'conf/steps/imputation_glimpse2.config'
+
+// validation step
+includeConfig 'conf/steps/validation.config'
+
 profiles {
     debug {
         dumpHashes              = true
@@ -322,27 +346,3 @@ validation {
         afterText = validation.help.afterText
     }
 }
-
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-
-// initialisation step
-includeConfig 'conf/steps/initialisation.config'
-
-// chrcheck workflow
-includeConfig 'conf/steps/chrcheck.config'
-
-// simulation step
-includeConfig 'conf/steps/simulation.config'
-
-// panel_prep step
-includeConfig 'conf/steps/panel_prep.config'
-
-// imputation step
-includeConfig 'conf/steps/imputation_glimpse1.config'
-includeConfig 'conf/steps/imputation_quilt.config'
-includeConfig 'conf/steps/imputation_stitch.config'
-includeConfig 'conf/steps/imputation_glimpse2.config'
-
-// validation step
-includeConfig 'conf/steps/validation.config'

From 8a7f9a154e7c3f5435083763ff3ccc0a90b3ef0a Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 17:57:43 +0100
Subject: [PATCH 05/17] Fix splitting operation

---
 conf/modules.config                           | 2 +-
 conf/steps/validation.config                  | 2 +-
 subworkflows/local/vcf_split_bcftools/main.nf | 5 +++--
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 2932d5f4..804a5c37 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -88,7 +88,7 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.tools}" }
+        ext.prefix = { "${meta.id}-batch${meta.batch}-${meta.tools}-" }
         publishDir = [
             path: { "${params.outdir}/imputation/${meta.tools}/samples/" },
             mode: params.publish_dir_mode,
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index 285221d6..3d5cc072 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -75,7 +75,7 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}.truth" }
+        ext.prefix = { "${meta.id}-truth-" }
     }
 
     // Validation subworkflow
diff --git a/subworkflows/local/vcf_split_bcftools/main.nf b/subworkflows/local/vcf_split_bcftools/main.nf
index 524b3e88..a0df60a6 100644
--- a/subworkflows/local/vcf_split_bcftools/main.nf
+++ b/subworkflows/local/vcf_split_bcftools/main.nf
@@ -13,11 +13,12 @@ workflow VCF_SPLIT_BCFTOOLS {
 
     ch_vcf_samples = BCFTOOLS_PLUGINSPLIT.out.vcf
         .transpose()
-        .map{metaITC, vcf -> [metaITC + [id: vcf.getBaseName().tokenize(".")[0]], vcf]}
+        .map{metaITC, vcf -> [metaITC + [id: vcf.getBaseName().tokenize(".")[0].tokenize("-")[-1]], vcf]}
 
     ch_tbi_samples = BCFTOOLS_PLUGINSPLIT.out.tbi
         .transpose()
-        .map{metaITC, tbi -> [metaITC + [id: tbi.getBaseName().tokenize(".")[0]], tbi]}
+        .view()
+        .map{metaITC, tbi -> [metaITC + [id: tbi.getBaseName().tokenize(".")[0].tokenize("-")[-1]], tbi]}
 
     ch_vcf_tbi_samples = ch_vcf_samples
         .join(ch_tbi_samples)

From 7846c23564364823171f786ddd74bbea5c40a0f9 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 18:01:21 +0100
Subject: [PATCH 06/17] Fix splitting operation

---
 conf/modules.config                           | 2 +-
 subworkflows/local/vcf_split_bcftools/main.nf | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 804a5c37..a6e466fd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -93,7 +93,7 @@ process {
             path: { "${params.outdir}/imputation/${meta.tools}/samples/" },
             mode: params.publish_dir_mode,
             enabled: true,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename.tokenize("-")[-1] }
         ]
     }
 
diff --git a/subworkflows/local/vcf_split_bcftools/main.nf b/subworkflows/local/vcf_split_bcftools/main.nf
index a0df60a6..2e6d741d 100644
--- a/subworkflows/local/vcf_split_bcftools/main.nf
+++ b/subworkflows/local/vcf_split_bcftools/main.nf
@@ -19,6 +19,7 @@ workflow VCF_SPLIT_BCFTOOLS {
         .transpose()
         .view()
         .map{metaITC, tbi -> [metaITC + [id: tbi.getBaseName().tokenize(".")[0].tokenize("-")[-1]], tbi]}
+        .view()
 
     ch_vcf_tbi_samples = ch_vcf_samples
         .join(ch_tbi_samples)

From 2eb5f0057e3ce3dd137dcc75770466e1dd4f70f8 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 18 Nov 2024 18:04:47 +0100
Subject: [PATCH 07/17] Fix splitting operation

---
 conf/steps/validation.config | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index 3d5cc072..38da7887 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -65,19 +65,16 @@ process {
     }
 
     // Split by samples
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:.*' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
+        ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
+        ext.prefix = { "${meta.id}-truth" }
         publishDir = [
             path: { "${params.outdir}/validation/samples" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename.tokenize("-")[-1] }
         ]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
-        ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}-truth-" }
-    }
-
     // Validation subworkflow
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:.*' {
         publishDir = [

From a2b15da10fe0ad2259efb30d2d1c3a4c7462cfc3 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Mon, 18 Nov 2024 23:02:20 +0100
Subject: [PATCH 08/17] Update truth split

---
 conf/steps/validation.config                  |  2 +-
 workflows/phaseimpute/tests/main.nf.test.snap | 54 +++++++++----------
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index 38da7887..ffe908e5 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -67,7 +67,7 @@ process {
     // Split by samples
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}-truth" }
+        ext.prefix = { "${meta.id}-truth-" }
         publishDir = [
             path: { "${params.outdir}/validation/samples" },
             mode: params.publish_dir_mode,
diff --git a/workflows/phaseimpute/tests/main.nf.test.snap b/workflows/phaseimpute/tests/main.nf.test.snap
index 336b9585..163e702c 100644
--- a/workflows/phaseimpute/tests/main.nf.test.snap
+++ b/workflows/phaseimpute/tests/main.nf.test.snap
@@ -130,15 +130,15 @@
                 "validation/TestQuality.txt",
                 "validation/concat/all.A-truth.vcf.gz",
                 "validation/concat/all.A-truth.vcf.gz.tbi",
-                "validation/samples/NA12878.truth.vcf.gz",
-                "validation/samples/NA12878.truth.vcf.gz.tbi",
-                "validation/samples/NA19401.truth.vcf.gz",
-                "validation/samples/NA19401.truth.vcf.gz.tbi",
-                "validation/samples/NA20359.truth.vcf.gz",
-                "validation/samples/NA20359.truth.vcf.gz.tbi",
-                "validation/stats/NA12878.truth.bcftools_stats.txt",
-                "validation/stats/NA19401.truth.bcftools_stats.txt",
-                "validation/stats/NA20359.truth.bcftools_stats.txt"
+                "validation/samples/NA12878.vcf.gz",
+                "validation/samples/NA12878.vcf.gz.tbi",
+                "validation/samples/NA19401.vcf.gz",
+                "validation/samples/NA19401.vcf.gz.tbi",
+                "validation/samples/NA20359.vcf.gz",
+                "validation/samples/NA20359.vcf.gz.tbi",
+                "validation/stats/NA12878.bcftools_stats.txt",
+                "validation/stats/NA19401.bcftools_stats.txt",
+                "validation/stats/NA20359.bcftools_stats.txt"
             ],
             "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]",
             [
@@ -178,15 +178,15 @@
                 "validation/NA19401_SNP.txt",
                 "validation/NA20359_SNP.txt",
                 "validation/TestQuality.txt",
-                "validation/samples/NA12878.truth.vcf.gz",
-                "validation/samples/NA12878.truth.vcf.gz.tbi",
-                "validation/samples/NA19401.truth.vcf.gz",
-                "validation/samples/NA19401.truth.vcf.gz.tbi",
-                "validation/samples/NA20359.truth.vcf.gz",
-                "validation/samples/NA20359.truth.vcf.gz.tbi",
-                "validation/stats/NA12878.truth.bcftools_stats.txt",
-                "validation/stats/NA19401.truth.bcftools_stats.txt",
-                "validation/stats/NA20359.truth.bcftools_stats.txt"
+                "validation/samples/NA12878.vcf.gz",
+                "validation/samples/NA12878.vcf.gz.tbi",
+                "validation/samples/NA19401.vcf.gz",
+                "validation/samples/NA19401.vcf.gz.tbi",
+                "validation/samples/NA20359.vcf.gz",
+                "validation/samples/NA20359.vcf.gz.tbi",
+                "validation/stats/NA12878.bcftools_stats.txt",
+                "validation/stats/NA19401.bcftools_stats.txt",
+                "validation/stats/NA20359.bcftools_stats.txt"
             ]
         ],
         "meta": {
@@ -256,15 +256,15 @@
                 "validation/NA20359_P1000GP_Tglimpse2_SNP.txt",
                 "validation/NA20359_P1000GP_Tquilt_SNP.txt",
                 "validation/TestQuality.txt",
-                "validation/samples/NA12878.truth.vcf.gz",
-                "validation/samples/NA12878.truth.vcf.gz.tbi",
-                "validation/samples/NA19401.truth.vcf.gz",
-                "validation/samples/NA19401.truth.vcf.gz.tbi",
-                "validation/samples/NA20359.truth.vcf.gz",
-                "validation/samples/NA20359.truth.vcf.gz.tbi",
-                "validation/stats/NA12878.truth.bcftools_stats.txt",
-                "validation/stats/NA19401.truth.bcftools_stats.txt",
-                "validation/stats/NA20359.truth.bcftools_stats.txt"
+                "validation/samples/NA12878.vcf.gz",
+                "validation/samples/NA12878.vcf.gz.tbi",
+                "validation/samples/NA19401.vcf.gz",
+                "validation/samples/NA19401.vcf.gz.tbi",
+                "validation/samples/NA20359.vcf.gz",
+                "validation/samples/NA20359.vcf.gz.tbi",
+                "validation/stats/NA12878.bcftools_stats.txt",
+                "validation/stats/NA19401.bcftools_stats.txt",
+                "validation/stats/NA20359.bcftools_stats.txt"
             ]
         ],
         "meta": {

From c1b7f1ee978750de86a26a58391019b8aff08bbe Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Mon, 18 Nov 2024 23:48:40 +0100
Subject: [PATCH 09/17] Update snap

---
 docs/output.md                                |  2 +-
 workflows/phaseimpute/tests/main.nf.test.snap | 38 ++-----------------
 2 files changed, 4 insertions(+), 36 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index 6e6777a4..55dc7321 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -168,7 +168,7 @@ The results from `--steps validate` will have the following directory structure:
   - `samples/*.vcf.gz`: A VCF of each truth sample.
   - `samples/*.vcf.gz.tbi`: A tbi for the truth VCF.
   - `stats/`:
-    - `*.truth.bcftools_stats.txt`: The statistics of the truth VCF target file produced by [`BCFTOOLS_STATS`](https://samtools.github.io/bcftools/bcftools.html#stats.)
+    - `*.bcftools_stats.txt`: The statistics of the truth VCF target file produced by [`BCFTOOLS_STATS`](https://samtools.github.io/bcftools/bcftools.html#stats.)
     - `*.P<panel name>_T<imputation tool>_SNP.txt`: Concordance metrics of the SNP variants obtained with [`GLIMPSE2_CONCORDANCE`](https://odelaneau.github.io/GLIMPSE/docs/documentation/concordance/).
     - `AllSamples.txt`: Aggregation of the above `GLIMPSE_CONCORDANCE` output across samples and tools.
 
diff --git a/workflows/phaseimpute/tests/main.nf.test.snap b/workflows/phaseimpute/tests/main.nf.test.snap
index b5d30026..383192e4 100644
--- a/workflows/phaseimpute/tests/main.nf.test.snap
+++ b/workflows/phaseimpute/tests/main.nf.test.snap
@@ -123,9 +123,6 @@
                 "validation/samples/NA19401.vcf.gz.tbi",
                 "validation/samples/NA20359.vcf.gz",
                 "validation/samples/NA20359.vcf.gz.tbi",
-                "validation/stats/NA12878.bcftools_stats.txt",
-                "validation/stats/NA19401.bcftools_stats.txt",
-                "validation/stats/NA20359.bcftools_stats.txt"
                 "validation/stats/AllSamples.txt",
                 "validation/stats/NA12878.truth.bcftools_stats.txt",
                 "validation/stats/NA12878_P1000GP_Tglimpse1_SNP.txt",
@@ -172,30 +169,17 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-17T21:32:08.538026091"
+        "timestamp": "2024-11-18T23:36:12.634065627"
     },
     "Check test_validate": {
         "content": [
             [
-                "validation/NA12878_SNP.txt",
-                "validation/NA19401_SNP.txt",
-                "validation/NA20359_SNP.txt",
-                "validation/TestQuality.txt",
                 "validation/samples/NA12878.vcf.gz",
                 "validation/samples/NA12878.vcf.gz.tbi",
                 "validation/samples/NA19401.vcf.gz",
                 "validation/samples/NA19401.vcf.gz.tbi",
                 "validation/samples/NA20359.vcf.gz",
                 "validation/samples/NA20359.vcf.gz.tbi",
-                "validation/stats/NA12878.bcftools_stats.txt",
-                "validation/stats/NA19401.bcftools_stats.txt",
-                "validation/stats/NA20359.bcftools_stats.txt"
-                "validation/samples/NA12878.truth.vcf.gz",
-                "validation/samples/NA12878.truth.vcf.gz.tbi",
-                "validation/samples/NA19401.truth.vcf.gz",
-                "validation/samples/NA19401.truth.vcf.gz.tbi",
-                "validation/samples/NA20359.truth.vcf.gz",
-                "validation/samples/NA20359.truth.vcf.gz.tbi",
                 "validation/stats/AllSamples.txt",
                 "validation/stats/NA12878.truth.bcftools_stats.txt",
                 "validation/stats/NA12878_SNP.txt",
@@ -209,7 +193,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-06T21:16:53.209347713"
+        "timestamp": "2024-11-18T23:30:21.177496237"
     },
     "Check test_batch": {
         "content": [
@@ -265,28 +249,12 @@
                 "NA20359"
             ],
             [
-                "validation/NA12878_P1000GP_Tglimpse2_SNP.txt",
-                "validation/NA12878_P1000GP_Tquilt_SNP.txt",
-                "validation/NA19401_P1000GP_Tglimpse2_SNP.txt",
-                "validation/NA19401_P1000GP_Tquilt_SNP.txt",
-                "validation/NA20359_P1000GP_Tglimpse2_SNP.txt",
-                "validation/NA20359_P1000GP_Tquilt_SNP.txt",
-                "validation/TestQuality.txt",
                 "validation/samples/NA12878.vcf.gz",
                 "validation/samples/NA12878.vcf.gz.tbi",
                 "validation/samples/NA19401.vcf.gz",
                 "validation/samples/NA19401.vcf.gz.tbi",
                 "validation/samples/NA20359.vcf.gz",
                 "validation/samples/NA20359.vcf.gz.tbi",
-                "validation/stats/NA12878.bcftools_stats.txt",
-                "validation/stats/NA19401.bcftools_stats.txt",
-                "validation/stats/NA20359.bcftools_stats.txt"
-                "validation/samples/NA12878.truth.vcf.gz",
-                "validation/samples/NA12878.truth.vcf.gz.tbi",
-                "validation/samples/NA19401.truth.vcf.gz",
-                "validation/samples/NA19401.truth.vcf.gz.tbi",
-                "validation/samples/NA20359.truth.vcf.gz",
-                "validation/samples/NA20359.truth.vcf.gz.tbi",
                 "validation/stats/AllSamples.txt",
                 "validation/stats/NA12878.truth.bcftools_stats.txt",
                 "validation/stats/NA12878_P1000GP_Tglimpse2_SNP.txt",
@@ -303,7 +271,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.0"
         },
-        "timestamp": "2024-11-06T21:03:44.505303287"
+        "timestamp": "2024-11-18T23:47:48.301571495"
     },
     "Check test_quilt": {
         "content": [

From eeb80375973d7a92d66206660cd8581ee1967a16 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 21 Nov 2024 16:19:40 +0100
Subject: [PATCH 10/17] Update bcftools pluginsplit

---
 conf/modules.config                           |  3 +-
 conf/steps/validation.config                  |  5 +--
 modules/nf-core/bcftools/pluginsplit/main.nf  | 42 ++++++-------------
 subworkflows/local/vcf_split_bcftools/main.nf |  6 +--
 4 files changed, 17 insertions(+), 39 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index a6e466fd..65d412dd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -88,12 +88,11 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}-batch${meta.batch}-${meta.tools}-" }
         publishDir = [
             path: { "${params.outdir}/imputation/${meta.tools}/samples/" },
             mode: params.publish_dir_mode,
             enabled: true,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename.tokenize("-")[-1] }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index a059b360..2c023a07 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -67,11 +67,10 @@ process {
     // Split by samples
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix = { "${meta.id}-truth-" }
         publishDir = [
             path: { "${params.outdir}/validation/samples" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename.tokenize("-")[-1] }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -102,6 +101,6 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GAWK' {
         ext.args2  = "'(NR == 1) || (FNR > 1)'" // Skip header line
         ext.suffix = { "txt" }
-        tag = {"Test Quality"}
+        tag = {"${meta.id}"}
     }
 }
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index df4145fe..082802be 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -15,19 +15,17 @@ process BCFTOOLS_PLUGINSPLIT {
     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 prefix = task.ext.prefix ?: "${meta.id}"
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -42,13 +40,9 @@ process BCFTOOLS_PLUGINSPLIT {
         ${groups_arg} \\
         ${regions_arg} \\
         ${targets_arg} \\
-        --output outputDir
+        --output ${prefix}
 
-    if [ -n "${prefix}" ]; then
-        for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\${file##*/}
-        done
-    fi
+    mv ${prefix}/* .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -58,7 +52,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -71,23 +65,11 @@ 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)" : ""
     """
-    mkdir -p outputDir
-
-    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/\$/.${index}/' <<< \$filename);
-            touch outputDir/\$index_file;
-        fi;
-    done < files.txt
-
-    if [ -n "${prefix}" ]; then
-        for file in outputDir/*; do
-            mv \$file outputDir/${prefix}\${file##*/}
-        done
-    fi
+    ${create_files}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/subworkflows/local/vcf_split_bcftools/main.nf b/subworkflows/local/vcf_split_bcftools/main.nf
index 2e6d741d..524b3e88 100644
--- a/subworkflows/local/vcf_split_bcftools/main.nf
+++ b/subworkflows/local/vcf_split_bcftools/main.nf
@@ -13,13 +13,11 @@ workflow VCF_SPLIT_BCFTOOLS {
 
     ch_vcf_samples = BCFTOOLS_PLUGINSPLIT.out.vcf
         .transpose()
-        .map{metaITC, vcf -> [metaITC + [id: vcf.getBaseName().tokenize(".")[0].tokenize("-")[-1]], vcf]}
+        .map{metaITC, vcf -> [metaITC + [id: vcf.getBaseName().tokenize(".")[0]], vcf]}
 
     ch_tbi_samples = BCFTOOLS_PLUGINSPLIT.out.tbi
         .transpose()
-        .view()
-        .map{metaITC, tbi -> [metaITC + [id: tbi.getBaseName().tokenize(".")[0].tokenize("-")[-1]], tbi]}
-        .view()
+        .map{metaITC, tbi -> [metaITC + [id: tbi.getBaseName().tokenize(".")[0]], tbi]}
 
     ch_vcf_tbi_samples = ch_vcf_samples
         .join(ch_tbi_samples)

From 0bd49f0f3fc8b5d491488e60c4ad87af43b3e7d2 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Fri, 22 Nov 2024 15:33:34 +0100
Subject: [PATCH 11/17] Update modules

---
 modules.json                                  |   7 +-
 .../pluginsplit/bcftools-pluginsplit.diff     |  22 ++++
 modules/nf-core/bcftools/pluginsplit/main.nf  |  21 ++--
 .../bcftools/pluginsplit/tests/main.nf.test   |  38 +++++--
 .../pluginsplit/tests/main.nf.test.snap       |  51 ++++++---
 .../bcftools/query}/environment.yml           |   2 +-
 modules/nf-core/bcftools/query/main.nf        |  56 ++++++++++
 modules/nf-core/bcftools/query/meta.yml       |  67 ++++++++++++
 .../nf-core/bcftools/query/tests/main.nf.test | 101 ++++++++++++++++++
 .../bcftools/query/tests/main.nf.test.snap    |  55 ++++++++++
 .../bcftools/query/tests/nextflow.config      |   3 +
 modules/nf-core/bcftools/query/tests/tags.yml |   2 +
 12 files changed, 390 insertions(+), 35 deletions(-)
 create mode 100644 modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
 rename modules/{local/list_to_file => nf-core/bcftools/query}/environment.yml (65%)
 create mode 100644 modules/nf-core/bcftools/query/main.nf
 create mode 100644 modules/nf-core/bcftools/query/meta.yml
 create mode 100644 modules/nf-core/bcftools/query/tests/main.nf.test
 create mode 100644 modules/nf-core/bcftools/query/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/bcftools/query/tests/nextflow.config
 create mode 100644 modules/nf-core/bcftools/query/tests/tags.yml

diff --git a/modules.json b/modules.json
index 6db896db..72f0a33e 100644
--- a/modules.json
+++ b/modules.json
@@ -46,10 +46,15 @@
                     },
                     "bcftools/pluginsplit": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "14c910af1f9c20c65e5df9325a1e4d3939d524d1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff"
                     },
+                    "bcftools/query": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/stats": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
diff --git a/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
new file mode 100644
index 00000000..5e3092d8
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/bcftools-pluginsplit.diff
@@ -0,0 +1,22 @@
+Changes in module 'nf-core/bcftools/pluginsplit'
+'modules/nf-core/bcftools/pluginsplit/environment.yml' is unchanged
+Changes in 'bcftools/pluginsplit/main.nf':
+--- modules/nf-core/bcftools/pluginsplit/main.nf
++++ modules/nf-core/bcftools/pluginsplit/main.nf
+@@ -8,8 +8,7 @@
+         'biocontainers/bcftools:1.20--h8b25389_0' }"
+ 
+     input:
+-    tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*")
+-    path(samples)
++    tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*"), path(samples)
+     path(groups)
+     path(regions)
+     path(targets)
+
+'modules/nf-core/bcftools/pluginsplit/meta.yml' is unchanged
+'modules/nf-core/bcftools/pluginsplit/tests/main.nf.test' is unchanged
+'modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap' is unchanged
+'modules/nf-core/bcftools/pluginsplit/tests/nextflow.config' is unchanged
+'modules/nf-core/bcftools/pluginsplit/tests/tags.yml' is unchanged
+************************************************************
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 082802be..d1977fbc 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -8,8 +8,7 @@ process BCFTOOLS_PLUGINSPLIT {
         'biocontainers/bcftools:1.20--h8b25389_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi)
-    path(samples)
+    tuple val(meta), path(vcf, stageAs: "input/*"), path(tbi, stageAs: "input/*"), path(samples)
     path(groups)
     path(regions)
     path(targets)
@@ -25,7 +24,6 @@ process BCFTOOLS_PLUGINSPLIT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
 
     def samples_arg = samples ? "--samples-file ${samples}" : ""
     def groups_arg  = groups  ? "--groups-file ${groups}"   : ""
@@ -40,9 +38,7 @@ process BCFTOOLS_PLUGINSPLIT {
         ${groups_arg} \\
         ${regions_arg} \\
         ${targets_arg} \\
-        --output ${prefix}
-
-    mv ${prefix}/* .
+        --output .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -52,7 +48,6 @@ process BCFTOOLS_PLUGINSPLIT {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
 
     def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
                 args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
@@ -65,11 +60,15 @@ 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}
+    cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
+    while IFS= read -r filename;
+        do ${create_cmd} "./\$filename";
+        if [ -n "${index}" ]; then
+            index_file=\$(sed -e 's/\$/.${index}/' <<< \$filename);
+            touch ./\$index_file;
+        fi;
+    done < files.txt
 
     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 e3160851..e7ae574e 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 {
@@ -91,16 +90,43 @@ nextflow_process {
             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") },
-                ) }
+                    process.out.vcf.collect{ it[1].collect { file(it).name } },
+                    process.out.tbi.collect{ it[1].collect { file(it).name } },
+                ).match() }
             )
         }
 
     }
 
-    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
+    test("homo_sapiens - [ vcf, tbi ], [], [], [], [], - error no sample") {
+        config "./nextflow.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: input/dbsnp_146.hg38.vcf.gz") }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
         options "-stub"
 
         when {
@@ -130,7 +156,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub") {
-
         options "-stub"
 
         when {
@@ -160,7 +185,6 @@ nextflow_process {
     }
 
     test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub") {
-
         config "./nextflow.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 66c3c1dd..b915b7cf 100644
--- a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -47,18 +47,39 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:42.307673651"
+        "timestamp": "2024-11-20T14:56:54.383979416"
+    },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi": {
+        "content": [
+            [
+                [
+                    "normal.vcf.gz",
+                    "tumour.vcf.gz"
+                ]
+            ],
+            [
+                [
+                    "normal.vcf.gz.tbi",
+                    "tumour.vcf.gz.tbi"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T14:56:44.796391578"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
         "content": null,
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:21.498991402"
+        "timestamp": "2024-11-20T14:56:36.709842966"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": {
         "content": [
@@ -126,10 +147,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:57:04.483688966"
+        "timestamp": "2024-11-20T14:57:11.163588435"
     },
     "homo_sapiens - [ vcf, tbi ], samples, [], [], []": {
         "content": [
@@ -179,10 +200,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:10.033818589"
+        "timestamp": "2024-11-20T14:56:27.978161766"
     },
     "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": {
         "content": [
@@ -232,9 +253,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-07-09T15:56:53.641165787"
+        "timestamp": "2024-11-20T14:57:02.456908152"
     }
 }
\ No newline at end of file
diff --git a/modules/local/list_to_file/environment.yml b/modules/nf-core/bcftools/query/environment.yml
similarity index 65%
rename from modules/local/list_to_file/environment.yml
rename to modules/nf-core/bcftools/query/environment.yml
index 315f6dc6..5c00b116 100644
--- a/modules/local/list_to_file/environment.yml
+++ b/modules/nf-core/bcftools/query/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::gawk=5.3.0
+  - bioconda::bcftools=1.20
diff --git a/modules/nf-core/bcftools/query/main.nf b/modules/nf-core/bcftools/query/main.nf
new file mode 100644
index 00000000..58019f4d
--- /dev/null
+++ b/modules/nf-core/bcftools/query/main.nf
@@ -0,0 +1,56 @@
+process BCFTOOLS_QUERY {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0':
+        'biocontainers/bcftools:1.20--h8b25389_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    path regions
+    path targets
+    path samples
+
+    output:
+    tuple val(meta), path("*.${suffix}"), emit: output
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.suffix ?: "txt"
+    def regions_file = regions ? "--regions-file ${regions}" : ""
+    def targets_file = targets ? "--targets-file ${targets}" : ""
+    def samples_file =  samples ? "--samples-file ${samples}" : ""
+    """
+    bcftools query \\
+        $regions_file \\
+        $targets_file \\
+        $samples_file \\
+        $args \\
+        $vcf \\
+        > ${prefix}.${suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    suffix = task.ext.suffix ?: "txt"
+    """
+    touch ${prefix}.${suffix} \\
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml
new file mode 100644
index 00000000..279b3205
--- /dev/null
+++ b/modules/nf-core/bcftools/query/meta.yml
@@ -0,0 +1,67 @@
+name: bcftools_query
+description: Extracts fields from VCF or BCF files and outputs them in user-defined
+  format.
+keywords:
+  - query
+  - variant calling
+  - bcftools
+  - VCF
+tools:
+  - query:
+      description: |
+        Extracts fields from VCF or BCF files and outputs them in user-defined format.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: biotools:bcftools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: |
+          The vcf file to be qeuried.
+        pattern: "*.{vcf.gz, vcf}"
+    - tbi:
+        type: file
+        description: |
+          The tab index for the VCF file to be inspected.
+        pattern: "*.tbi"
+  - - regions:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file.
+  - - targets:
+        type: file
+        description: |
+          Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
+  - - samples:
+        type: file
+        description: |
+          Optional, file of sample names to be included or excluded.
+          e.g. 'file.tsv'
+output:
+  - output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${suffix}":
+          type: file
+          description: BCFTools query output file
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@drpatelh"
+maintainers:
+  - "@abhi18av"
+  - "@drpatelh"
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test b/modules/nf-core/bcftools/query/tests/main.nf.test
new file mode 100644
index 00000000..39e67b35
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_QUERY"
+    script "../main.nf"
+    process "BCFTOOLS_QUERY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/query"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - [vcf, tbi], [], [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'out' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.output,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi], vcf, tsv, []") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'out' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true)
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.output,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [vcf, tbi], [], [], [] - stub") {
+
+        when {
+            process {
+                """
+                input[0] = [ 
+                    [ id:'out' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.output[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bcftools/query/tests/main.nf.test.snap b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
new file mode 100644
index 00000000..3ead1f2c
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/main.nf.test.snap
@@ -0,0 +1,55 @@
+{
+    "sarscov2 - [vcf, tbi], vcf, tsv, []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "out"
+                    },
+                    "out.txt:md5,75a6bd0084e2e1838cf7baba11b99d19"
+                ]
+            ],
+            [
+                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-31T15:15:44.916249758"
+    },
+    "sarscov2 - [vcf, tbi], [], [], [] - stub": {
+        "content": [
+            "out.txt",
+            [
+                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-31T15:15:49.932359271"
+    },
+    "sarscov2 - [vcf, tbi], [], [], []": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "out"
+                    },
+                    "out.txt:md5,87a2ab194e1ee3219b44e58429ec3307"
+                ]
+            ],
+            [
+                "versions.yml:md5,3d93ea9cd5d314743254618b49e4bd16"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-31T15:15:39.930697926"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/query/tests/nextflow.config b/modules/nf-core/bcftools/query/tests/nextflow.config
new file mode 100644
index 00000000..da81c2a0
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = "-f '%CHROM %POS %REF %ALT[%SAMPLE=%GT]'"
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/query/tests/tags.yml b/modules/nf-core/bcftools/query/tests/tags.yml
new file mode 100644
index 00000000..fb9455cb
--- /dev/null
+++ b/modules/nf-core/bcftools/query/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/query:
+  - "modules/nf-core/bcftools/query/**"

From c1fd1868f249942d4708c90424de22e11fc4183f Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Fri, 22 Nov 2024 15:42:34 +0100
Subject: [PATCH 12/17] Update vcf_split_bcftools

---
 subworkflows/local/vcf_split_bcftools/main.nf |  4 ++--
 .../vcf_split_bcftools/tests/main.nf.test     | 17 +++++++++-----
 .../tests/main.nf.test.snap                   | 22 +++++++++----------
 3 files changed, 25 insertions(+), 18 deletions(-)

diff --git a/subworkflows/local/vcf_split_bcftools/main.nf b/subworkflows/local/vcf_split_bcftools/main.nf
index 524b3e88..72832214 100644
--- a/subworkflows/local/vcf_split_bcftools/main.nf
+++ b/subworkflows/local/vcf_split_bcftools/main.nf
@@ -2,13 +2,13 @@ include { BCFTOOLS_PLUGINSPLIT  } from '../../../modules/nf-core/bcftools/plugin
 
 workflow VCF_SPLIT_BCFTOOLS {
     take:
-    ch_vcf          // channel: [ [id, chr, tools], vcf, index ]
+    ch_vcf          // channel: [ [id, chr, tools], vcf, index, samples ]
 
     main:
 
     ch_versions = Channel.empty()
 
-    BCFTOOLS_PLUGINSPLIT(ch_vcf, [], [], [], [])
+    BCFTOOLS_PLUGINSPLIT(ch_vcf, [], [], [])
     ch_versions = ch_versions.mix(BCFTOOLS_PLUGINSPLIT.out.versions.first())
 
     ch_vcf_samples = BCFTOOLS_PLUGINSPLIT.out.vcf
diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
index 1864bb76..b85b2be9 100644
--- a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
+++ b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_workflow {
     tag "bcftools"
     tag "bcftools/split"
 
-    test("Split multiple vcf file") {
+    test("Split multiple vcf file - with renaming") {
         setup {
             run("BCFTOOLS_MERGE") {
                 script "../../../../modules/nf-core/bcftools/merge/main.nf"
@@ -45,7 +45,12 @@ nextflow_workflow {
         when {
             workflow {
                 """
-                input[0] = BCFTOOLS_MERGE.out.vcf.join(BCFTOOLS_MERGE.out.tbi)
+                renaming_file = channel.of(
+                    "NA12878\tNA12878_test NA12878.myfile",
+                    "NA19401\t-\tNA19401",
+                    "NA20359\tNA20359_2\tNA20359_3"
+                ).collectFile(name: "samples.txt", newLine: true)
+                input[0] = BCFTOOLS_MERGE.out.vcf.join(BCFTOOLS_MERGE.out.tbi).combine(renaming_file)
                 """
             }
         }
@@ -78,7 +83,8 @@ nextflow_workflow {
                 input[0] = Channel.of([
                     [id: 'NA12878'],
                     file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf", checkIfExist:true),
-                    file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf.csi", checkIfExist:true)
+                    file(params.pipelines_testdata_base_path + "hum_data/individuals/NA12878/NA12878.s_imputed.bcf.csi", checkIfExist:true),
+                    []
                 ])
                 """
             }
@@ -106,7 +112,8 @@ nextflow_workflow {
                 input[0] = Channel.of([
                     [id: 'dbsnp_146.hg38'],
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz", checkIfExist:true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExist:true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi", checkIfExist:true),
+                    []
                 ])
                 """
             }
@@ -115,7 +122,7 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.failed },
-                { assert workflow.errorReport.contains("No samples to split: dbsnp_146.hg38.vcf.gz")
+                { assert workflow.errorReport.contains("No samples to split: input/dbsnp_146.hg38.vcf.gz")
                 }
             )
         }
diff --git a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
index 02a8da3a..d6084e40 100644
--- a/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
+++ b/subworkflows/local/vcf_split_bcftools/tests/main.nf.test.snap
@@ -16,11 +16,11 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-13T14:06:59.745818945"
+        "timestamp": "2024-11-22T13:53:09.194659411"
     },
-    "Split multiple vcf file": {
+    "Split multiple vcf file - with renaming": {
         "content": [
             [
                 "versions.yml:md5,6c3351d97e3a99f7a7a3231fc49f92e2"
@@ -30,8 +30,8 @@
                     {
                         "id": "NA12878"
                     },
-                    "NA12878.vcf.gz",
-                    "NA12878.vcf.gz.tbi"
+                    "NA12878.myfile.vcf.gz",
+                    "NA12878.myfile.vcf.gz.tbi"
                 ],
                 [
                     {
@@ -42,10 +42,10 @@
                 ],
                 [
                     {
-                        "id": "NA20359"
+                        "id": "NA20359_3"
                     },
-                    "NA20359.vcf.gz",
-                    "NA20359.vcf.gz.tbi"
+                    "NA20359_3.vcf.gz",
+                    "NA20359_3.vcf.gz.tbi"
                 ]
             ],
             [
@@ -56,8 +56,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-11T14:42:48.076610625"
+        "timestamp": "2024-11-22T13:53:01.127637055"
     }
-}
+}
\ No newline at end of file

From cd450c313f8178ab4307ccccaa2181d512a3a6f4 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Fri, 22 Nov 2024 15:43:39 +0100
Subject: [PATCH 13/17] Add samples renaming for truth splitted files

---
 conf/steps/validation.config                  | 14 ++++
 conf/test.config                              |  2 +-
 conf/test_all.config                          |  2 +-
 workflows/phaseimpute/main.nf                 | 11 ++-
 workflows/phaseimpute/tests/main.nf.test.snap | 72 +++++++++----------
 5 files changed, 61 insertions(+), 40 deletions(-)

diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index 2c023a07..3a9b85cb 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -64,6 +64,20 @@ process {
         ext.args   = ["--ligate", "--output-type z", "--write-index=tbi"].join(' ')
     }
 
+    // Compute sample files for renaming
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_QUERY' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.args = '--list-samples'
+        publishDir = [enabled: false]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GAWK' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.prefix = { "${meta.id}_samples"}
+        ext.args2 = "'BEGIN { OFS = \"\\t\" } { print \$1, \"-\", \$1\".truth\" }'"
+        publishDir = [enabled: false]
+    }
+
     // Split by samples
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_TRUTH:BCFTOOLS_PLUGINSPLIT' {
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
diff --git a/conf/test.config b/conf/test.config
index f5c7b8dd..d3d19505 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -13,7 +13,7 @@
 process {
     resourceLimits = [
         cpus: 4,
-        memory: '15.GB',
+        memory: '7.GB',
         time: '1.h'
     ]
 }
diff --git a/conf/test_all.config b/conf/test_all.config
index c16d7904..fc2e845f 100644
--- a/conf/test_all.config
+++ b/conf/test_all.config
@@ -13,7 +13,7 @@
 process {
     resourceLimits = [
         cpus: 2,
-        memory: '10.GB',
+        memory: '7.GB',
         time: '1.h'
     ]
 }
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 4ca49bea..34ea9e40 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -65,6 +65,8 @@ include { BCFTOOLS_STATS as BCFTOOLS_STATS_TOOLS     } from '../../modules/nf-co
 
 // Concordance subworkflows
 include { BAM_GL_BCFTOOLS as GL_TRUTH                } from '../../subworkflows/local/bam_gl_bcftools'
+include { BCFTOOLS_QUERY                             } from '../../modules/nf-core/bcftools/query'
+include { GAWK                                       } from '../../modules/nf-core/gawk'
 include { VCF_SPLIT_BCFTOOLS as SPLIT_TRUTH          } from '../../subworkflows/local/vcf_split_bcftools'
 include { BCFTOOLS_STATS as BCFTOOLS_STATS_TRUTH     } from '../../modules/nf-core/bcftools/stats'
 include { VCF_CONCATENATE_BCFTOOLS as CONCAT_TRUTH   } from '../../subworkflows/local/vcf_concatenate_bcftools'
@@ -372,7 +374,7 @@ workflow PHASEIMPUTE {
         }
 
         // Split result by samples
-        VCF_SPLIT_BCFTOOLS(ch_input_validate)
+        VCF_SPLIT_BCFTOOLS(ch_input_validate.map{ [it[0], it[1], it[2], []] })
         ch_input_validate = VCF_SPLIT_BCFTOOLS.out.vcf_tbi
 
         // Compute stats on imputed files
@@ -443,8 +445,13 @@ workflow PHASEIMPUTE {
         CONCAT_TRUTH(ch_truth_vcf)
         ch_versions = ch_versions.mix(CONCAT_TRUTH.out.versions)
 
+        // Prepare renaming file
+        BCFTOOLS_QUERY(CONCAT_TRUTH.out.vcf_tbi, [], [], [])
+        GAWK(BCFTOOLS_QUERY.out.output, [])
+        ch_pluginsplit = CONCAT_TRUTH.out.vcf_tbi.join(GAWK.out.output.view())
+
         // Split truth vcf by samples
-        SPLIT_TRUTH(CONCAT_TRUTH.out.vcf_tbi)
+        SPLIT_TRUTH(ch_pluginsplit)
         ch_versions = ch_versions.mix(SPLIT_TRUTH.out.versions)
 
         // Compute stats on truth files
diff --git a/workflows/phaseimpute/tests/main.nf.test.snap b/workflows/phaseimpute/tests/main.nf.test.snap
index 383192e4..ed71c96a 100644
--- a/workflows/phaseimpute/tests/main.nf.test.snap
+++ b/workflows/phaseimpute/tests/main.nf.test.snap
@@ -25,10 +25,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-25T16:47:19.203956394"
+        "timestamp": "2024-11-22T13:07:42.012993182"
     },
     "Check test_all": {
         "content": [
@@ -117,12 +117,12 @@
             [
                 "validation/concat/all.A-truth.vcf.gz",
                 "validation/concat/all.A-truth.vcf.gz.tbi",
-                "validation/samples/NA12878.vcf.gz",
-                "validation/samples/NA12878.vcf.gz.tbi",
-                "validation/samples/NA19401.vcf.gz",
-                "validation/samples/NA19401.vcf.gz.tbi",
-                "validation/samples/NA20359.vcf.gz",
-                "validation/samples/NA20359.vcf.gz.tbi",
+                "validation/samples/NA12878.truth.vcf.gz",
+                "validation/samples/NA12878.truth.vcf.gz.tbi",
+                "validation/samples/NA19401.truth.vcf.gz",
+                "validation/samples/NA19401.truth.vcf.gz.tbi",
+                "validation/samples/NA20359.truth.vcf.gz",
+                "validation/samples/NA20359.truth.vcf.gz.tbi",
                 "validation/stats/AllSamples.txt",
                 "validation/stats/NA12878.truth.bcftools_stats.txt",
                 "validation/stats/NA12878_P1000GP_Tglimpse1_SNP.txt",
@@ -167,19 +167,19 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T23:36:12.634065627"
+        "timestamp": "2024-11-22T13:58:54.188813202"
     },
     "Check test_validate": {
         "content": [
             [
-                "validation/samples/NA12878.vcf.gz",
-                "validation/samples/NA12878.vcf.gz.tbi",
-                "validation/samples/NA19401.vcf.gz",
-                "validation/samples/NA19401.vcf.gz.tbi",
-                "validation/samples/NA20359.vcf.gz",
-                "validation/samples/NA20359.vcf.gz.tbi",
+                "validation/samples/NA12878.truth.vcf.gz",
+                "validation/samples/NA12878.truth.vcf.gz.tbi",
+                "validation/samples/NA19401.truth.vcf.gz",
+                "validation/samples/NA19401.truth.vcf.gz.tbi",
+                "validation/samples/NA20359.truth.vcf.gz",
+                "validation/samples/NA20359.truth.vcf.gz.tbi",
                 "validation/stats/AllSamples.txt",
                 "validation/stats/NA12878.truth.bcftools_stats.txt",
                 "validation/stats/NA12878_SNP.txt",
@@ -191,9 +191,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T23:30:21.177496237"
+        "timestamp": "2024-11-22T13:54:09.435194577"
     },
     "Check test_batch": {
         "content": [
@@ -249,12 +249,12 @@
                 "NA20359"
             ],
             [
-                "validation/samples/NA12878.vcf.gz",
-                "validation/samples/NA12878.vcf.gz.tbi",
-                "validation/samples/NA19401.vcf.gz",
-                "validation/samples/NA19401.vcf.gz.tbi",
-                "validation/samples/NA20359.vcf.gz",
-                "validation/samples/NA20359.vcf.gz.tbi",
+                "validation/samples/NA12878.truth.vcf.gz",
+                "validation/samples/NA12878.truth.vcf.gz.tbi",
+                "validation/samples/NA19401.truth.vcf.gz",
+                "validation/samples/NA19401.truth.vcf.gz.tbi",
+                "validation/samples/NA20359.truth.vcf.gz",
+                "validation/samples/NA20359.truth.vcf.gz.tbi",
                 "validation/stats/AllSamples.txt",
                 "validation/stats/NA12878.truth.bcftools_stats.txt",
                 "validation/stats/NA12878_P1000GP_Tglimpse2_SNP.txt",
@@ -269,9 +269,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.0"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-18T23:47:48.301571495"
+        "timestamp": "2024-11-22T14:06:57.642618122"
     },
     "Check test_quilt": {
         "content": [
@@ -299,10 +299,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-25T16:46:11.131198832"
+        "timestamp": "2024-11-22T13:05:58.709941089"
     },
     "Check test_sim": {
         "content": [
@@ -380,10 +380,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-25T16:44:41.049965503"
+        "timestamp": "2024-11-22T13:03:28.516026252"
     },
     "Check test": {
         "content": [
@@ -463,9 +463,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-25T16:56:33.72923425"
+        "timestamp": "2024-11-22T13:16:12.803136748"
     }
 }
\ No newline at end of file

From 2e540952f61aa036cc07c8fac00689bfdc069b93 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Fri, 22 Nov 2024 15:48:00 +0100
Subject: [PATCH 14/17] Reset changes

---
 conf/test.config     | 2 +-
 conf/test_all.config | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index d3d19505..f5c7b8dd 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -13,7 +13,7 @@
 process {
     resourceLimits = [
         cpus: 4,
-        memory: '7.GB',
+        memory: '15.GB',
         time: '1.h'
     ]
 }
diff --git a/conf/test_all.config b/conf/test_all.config
index fc2e845f..c16d7904 100644
--- a/conf/test_all.config
+++ b/conf/test_all.config
@@ -13,7 +13,7 @@
 process {
     resourceLimits = [
         cpus: 2,
-        memory: '7.GB',
+        memory: '10.GB',
         time: '1.h'
     ]
 }

From ca67cbb9ad8f67a2446a930df101f1905ff1dce3 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Fri, 22 Nov 2024 15:49:47 +0100
Subject: [PATCH 15/17] Reset changes

---
 docs/output.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index 55dc7321..6e6777a4 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -168,7 +168,7 @@ The results from `--steps validate` will have the following directory structure:
   - `samples/*.vcf.gz`: A VCF of each truth sample.
   - `samples/*.vcf.gz.tbi`: A tbi for the truth VCF.
   - `stats/`:
-    - `*.bcftools_stats.txt`: The statistics of the truth VCF target file produced by [`BCFTOOLS_STATS`](https://samtools.github.io/bcftools/bcftools.html#stats.)
+    - `*.truth.bcftools_stats.txt`: The statistics of the truth VCF target file produced by [`BCFTOOLS_STATS`](https://samtools.github.io/bcftools/bcftools.html#stats.)
     - `*.P<panel name>_T<imputation tool>_SNP.txt`: Concordance metrics of the SNP variants obtained with [`GLIMPSE2_CONCORDANCE`](https://odelaneau.github.io/GLIMPSE/docs/documentation/concordance/).
     - `AllSamples.txt`: Aggregation of the above `GLIMPSE_CONCORDANCE` output across samples and tools.
 

From 46464ebb172f3bba932183b8e53934746c554805 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Fri, 22 Nov 2024 15:51:57 +0100
Subject: [PATCH 16/17] Reset changes

---
 modules/local/list_to_file/environment.yml | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 modules/local/list_to_file/environment.yml

diff --git a/modules/local/list_to_file/environment.yml b/modules/local/list_to_file/environment.yml
new file mode 100644
index 00000000..315f6dc6
--- /dev/null
+++ b/modules/local/list_to_file/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::gawk=5.3.0

From d3aac0c486fc6fb2d7f71de96b83b6ac21440f8a Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gamil.com>
Date: Sat, 23 Nov 2024 15:51:26 +0100
Subject: [PATCH 17/17] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6cea3088..3a1b8d40 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -74,6 +74,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
 - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV.
 - [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`.
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
+- [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 
 ### `Dependencies`