diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index d77a1c64..2d015336 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -18,7 +18,7 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_VER: "0.9.3"
+  NFT_VER: "0.9.5"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
@@ -90,7 +90,6 @@ jobs:
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test
-        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
           NXF_VERSION: ${{ matrix.NXF_VER }}
diff --git a/main.nf b/main.nf
index c8d77c79..32ee9feb 100644
--- a/main.nf
+++ b/main.nf
@@ -154,16 +154,14 @@ output {
     }
     sample_vcfs {
         path { meta, vcf, tbi ->
-            def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            vcf >> "${base}.vcf.gz"
-            tbi >> "${base}.vcf.gz.tbi"
+            vcf >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz"
+            tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi"
         }
     }
     family_vcfs {
         path { meta, vcf, tbi ->
-            def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            vcf >> "${base}.vcf.gz"
-            tbi >> "${base}.vcf.gz.tbi"
+            vcf >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz"
+            tbi >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".vcf.gz.tbi"
         }
     }
     qdnaseq_out {
@@ -186,8 +184,7 @@ output {
     }
     bedpe {
         path { meta, bedpe ->
-            def base = "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}"
-            bedpe >> "${base}.bedpe"
+            bedpe >> "${meta.id}/${meta.id}${meta.variant_type ? '.' + meta.variant_type : ''}" + ".bedpe"
         }
     }
     multiqc {
diff --git a/modules.json b/modules.json
index 9c5d969b..6466f4ea 100644
--- a/modules.json
+++ b/modules.json
@@ -99,7 +99,7 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
+                        "git_sha": "156feda0cb6589cd29c04902004fa3b53bc00205",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
index 89e12a64..946bb362 100644
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -5,6 +5,6 @@ channels:
   - bioconda
 dependencies:
   # renovate: datasource=conda depName=bioconda/htslib
-  - bioconda::htslib=1.22.1
+  - bioconda::htslib=1.23.1
   # renovate: datasource=conda depName=bioconda/samtools
-  - bioconda::samtools=1.22.1
+  - bioconda::samtools=1.23.1
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index 97bfb578..4ff3fd70 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -1,21 +1,21 @@
 process SAMTOOLS_FAIDX {
-    tag "$fasta"
+    tag "${fasta}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' :
-        'biocontainers/samtools:1.22.1--h96c455f_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c5d2818c8b9f58e1fba77ce219fdaf32087ae53e857c4a496402978af26e78c/data'
+        : 'community.wave.seqera.io/library/htslib_samtools:1.23.1--5b6bb4ede7e612e5'}"
 
     input:
     tuple val(meta), path(fasta), path(fai)
     val get_sizes
 
     output:
-    tuple val(meta), path ("*.{fa,fasta}") , emit: fa, optional: true
-    tuple val(meta), path ("*.sizes")      , emit: sizes, optional: true
-    tuple val(meta), path ("*.fai")        , emit: fai, optional: true
-    tuple val(meta), path ("*.gzi")        , emit: gzi, optional: true
+    tuple val(meta), path("*.{fa,fasta}"), emit: fa, optional: true
+    tuple val(meta), path("*.sizes"), emit: sizes, optional: true
+    tuple val(meta), path("*.fai"), emit: fai, optional: true
+    tuple val(meta), path("*.gzi"), emit: gzi, optional: true
     tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
 
     when:
@@ -27,8 +27,8 @@ process SAMTOOLS_FAIDX {
     """
     samtools \\
         faidx \\
-        $fasta \\
-        $args
+        ${fasta} \\
+        ${args}
 
     ${get_sizes_command}
     """
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index 80aae1da..529f7a26 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -110,3 +110,4 @@ authors:
 maintainers:
   - "@maxulysse"
   - "@phue"
+  - "@matthdsm"
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
index 41697444..e879d962 100644
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
@@ -23,16 +23,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:39:12.541649151"
+        "timestamp": "2026-03-19T08:57:29.747964"
     },
     "test_samtools_faidx_get_sizes_bgzip - stub": {
         "content": [
@@ -68,16 +68,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:41:44.040426987"
+        "timestamp": "2026-03-19T08:58:10.04235"
     },
     "test_samtools_faidx_get_sizes": {
         "content": [
@@ -108,16 +108,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:47:03.653912015"
+        "timestamp": "2026-03-19T08:57:55.552612"
     },
     "test_samtools_faidx_bgzip": {
         "content": [
@@ -148,16 +148,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:50:04.023566795"
+        "timestamp": "2026-03-19T08:57:34.346045"
     },
     "test_samtools_faidx_fasta": {
         "content": [
@@ -183,16 +183,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:39:23.529404162"
+        "timestamp": "2026-03-19T08:57:39.136814"
     },
     "test_samtools_faidx_get_sizes - stub": {
         "content": [
@@ -223,16 +223,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:41:39.039834304"
+        "timestamp": "2026-03-19T08:58:05.200994"
     },
     "test_samtools_faidx_stub_fasta": {
         "content": [
@@ -258,16 +258,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:39:28.961701609"
+        "timestamp": "2026-03-19T08:57:44.105654"
     },
     "test_samtools_faidx_stub_fai": {
         "content": [
@@ -293,16 +293,16 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:39:34.471028474"
+        "timestamp": "2026-03-19T08:57:50.839162"
     },
     "test_samtools_faidx_get_sizes_bgzip": {
         "content": [
@@ -338,15 +338,15 @@
                     [
                         "SAMTOOLS_FAIDX",
                         "samtools",
-                        "1.22.1"
+                        "1.23.1"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-02-10T15:39:45.439016495"
+        "timestamp": "2026-03-19T08:58:00.460031"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config
index 202c036e..b3c4d0cb 100644
--- a/modules/nf-core/samtools/faidx/tests/nextflow.config
+++ b/modules/nf-core/samtools/faidx/tests/nextflow.config
@@ -3,5 +3,4 @@ process {
     withName: SAMTOOLS_FAIDX {
         ext.args = params.module_args
     }
-
 }
diff --git a/tests/lib/Utils.groovy b/tests/lib/Utils.groovy
new file mode 100644
index 00000000..5de44c1d
--- /dev/null
+++ b/tests/lib/Utils.groovy
@@ -0,0 +1,18 @@
+import java.nio.file.Path
+import groovy.transform.CompileDynamic
+
+/**
+ * Utility functions for testing.
+ */
+@CompileDynamic
+class Utils {
+
+    static Object getRecursiveFileNames(Path fileOrDir, String outputDir) {
+        /* groovylint-disable-next-line UnnecessaryGetter */
+        if (Path.of(fileOrDir.toString()).toFile().isDirectory()) {
+            return fileOrDir.list().collect { file -> getRecursiveFileNames(file, outputDir) }
+        }
+        return fileOrDir.toString().replace("${outputDir}/", '')
+    }
+
+}
diff --git a/tests/pipeline/all_types/all.nf.test b/tests/pipeline/all_types/all.nf.test
index 7209442e..59771a36 100644
--- a/tests/pipeline/all_types/all.nf.test
+++ b/tests/pipeline/all_types/all.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     path("$outputDir")
                         .list()
                         .findAll { !it.toString().endsWith("pipeline_info") }
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                 ).match("all")}
             )
@@ -55,7 +55,7 @@ nextflow_pipeline {
                     path("$outputDir")
                         .list()
                         .findAll { !it.toString().endsWith("pipeline_info") }
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                 ).match("concat")}
             )
@@ -83,7 +83,7 @@ nextflow_pipeline {
                     path("$outputDir")
                         .list()
                         .findAll { !it.toString().endsWith("pipeline_info") }
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                 ).match("output callers")}
             )
@@ -92,10 +92,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/tests/pipeline/bedpe/bedpe.nf.test b/tests/pipeline/bedpe/bedpe.nf.test
index 7a5635ff..f0159431 100644
--- a/tests/pipeline/bedpe/bedpe.nf.test
+++ b/tests/pipeline/bedpe/bedpe.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -79,7 +79,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -91,10 +91,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/tests/pipeline/cnv/cnv.nf.test b/tests/pipeline/cnv/cnv.nf.test
index 146dd6f6..cd5a62c3 100644
--- a/tests/pipeline/cnv/cnv.nf.test
+++ b/tests/pipeline/cnv/cnv.nf.test
@@ -26,7 +26,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -55,7 +55,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -67,10 +67,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/tests/pipeline/duplicates/duplicates.nf.test b/tests/pipeline/duplicates/duplicates.nf.test
index e403463d..8e36bba5 100644
--- a/tests/pipeline/duplicates/duplicates.nf.test
+++ b/tests/pipeline/duplicates/duplicates.nf.test
@@ -26,7 +26,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -38,10 +38,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/tests/pipeline/families/families.nf.test b/tests/pipeline/families/families.nf.test
index a008142b..e411af99 100644
--- a/tests/pipeline/families/families.nf.test
+++ b/tests/pipeline/families/families.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -58,7 +58,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -88,7 +88,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -119,7 +119,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -131,10 +131,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/tests/pipeline/repeats/repeats.nf.test b/tests/pipeline/repeats/repeats.nf.test
index c12dc262..cf42df68 100644
--- a/tests/pipeline/repeats/repeats.nf.test
+++ b/tests/pipeline/repeats/repeats.nf.test
@@ -26,7 +26,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -38,10 +38,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/tests/pipeline/sv/sv.nf.test b/tests/pipeline/sv/sv.nf.test
index 77957627..679ed811 100644
--- a/tests/pipeline/sv/sv.nf.test
+++ b/tests/pipeline/sv/sv.nf.test
@@ -26,7 +26,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -55,7 +55,7 @@ nextflow_pipeline {
                 { assert snapshot(
                     path("${outputDir}")
                         .list()
-                        .collect { getRecursiveFileNames(it, "${outputDir}") }
+                        .collect { Utils.getRecursiveFileNames(it, "${outputDir}") }
                         .flatten()
                         .findAll {
                             !it.contains("pipeline_info/")
@@ -67,10 +67,3 @@ nextflow_pipeline {
     }
 
 }
-
-def getRecursiveFileNames(fileOrDir, outputDir) {
-    if(file(fileOrDir.toString()).isDirectory()) {
-        return fileOrDir.list().collect { getRecursiveFileNames(it, outputDir) }
-    }
-    return fileOrDir.toString().replace("${outputDir}/", "")
-}
diff --git a/workflows/structural.nf b/workflows/structural.nf
index 384036ca..ed99d1fc 100644
--- a/workflows/structural.nf
+++ b/workflows/structural.nf
@@ -196,8 +196,8 @@ workflow STRUCTURAL {
     def ch_fai = channel.empty()
     if(!fai){
         SAMTOOLS_FAIDX(
-            ch_fasta,
-            [[], []]
+            ch_fasta.map { meta, f -> [ meta, f, [] ]},
+            false
         )
         ch_fai      = SAMTOOLS_FAIDX.out.fai.collect { fai_file -> [[id:'reference'], fai_file] }
     }