From 73a15fef58a02877e7946aa6ab0e89dd8548384f Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 25 Mar 2026 13:22:43 +0000
Subject: [PATCH 01/15] Update bioawk

---
 modules/nf-core/bioawk/main.nf                | 27 +++++--
 modules/nf-core/bioawk/meta.yml               | 50 ++++++++----
 modules/nf-core/bioawk/tests/main.nf.test     | 31 +++++++-
 .../nf-core/bioawk/tests/main.nf.test.snap    | 77 +++++++++++++++++--
 modules/nf-core/bioawk/tests/nextflow.config  |  2 +-
 .../tests/nextflow_telomere_check.config      |  6 ++
 6 files changed, 159 insertions(+), 34 deletions(-)
 create mode 100644 modules/nf-core/bioawk/tests/nextflow_telomere_check.config

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 70780b3db8e4..211bf78ffe0d 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -1,5 +1,5 @@
 process BIOAWK {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
@@ -9,9 +9,12 @@ process BIOAWK {
 
     input:
     tuple val(meta), path(input)
+    val suffix
+    val zip_bool
 
     output:
-    tuple val(meta), path("*.gz"), emit: output
+    tuple val(meta), path("${file_output}"),    optional: true, emit: output
+    tuple val(meta), path("*.gz"),              optional: true, emit: gz_output
     tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions
     // WARN: Version information not provided by tool on CLI. Please update version string above when bumping container versions.
 
@@ -19,16 +22,26 @@ process BIOAWK {
     task.ext.when == null || task.ext.when
 
     script:
-    def args  = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("${input}" == "${prefix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate."
+    def args        = task.ext.args ?: ''
+    def prefix      = task.ext.prefix ?: "${meta.id}"
+    file_output     = "${prefix}.${suffix}"
+    if ("${input}" == "${file_output}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate."
 
     """
     bioawk \
         $args \
         $input \
-        > ${prefix}
+        > ${file_output}
 
-    gzip ${prefix}
+    if [ "${zip_bool}" = "true" ]; then
+        gzip "${file_output}"
+    fi
+
+    """
+
+    stub:
+    """
+    touch ${file_output}
+    echo "" > ${file_output}.gz
     """
 }
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index 5bea6172672b..8e3a70df608b 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -1,7 +1,6 @@
-schema_version: 1.1.0
 name: "bioawk"
-description: Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.
-
+description: Bioawk is an extension to Brian Kernighan's awk, adding the support
+  of several common biological data formats.
 keywords:
   - bioawk
   - fastq
@@ -9,7 +8,6 @@ keywords:
   - sam
   - file manipulation
   - awk
-
 tools:
   - bioawk:
       description: BWK awk modified for biological data
@@ -17,9 +15,9 @@ tools:
       documentation: https://github.com/lh3/bioawk
       tool_dev_url: https://github.com/lh3/bioawk
       licence:
-        - Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)
+        - Free software license
+          (https://github.com/lh3/bioawk/blob/master/README.awk#L1)
       identifier: ""
-
 input:
   - - meta:
         type: map
@@ -31,9 +29,28 @@ input:
         description: |
           Input biological sequence file (optionally gzipped) to be manipulated via the program specified in `$args`.
         pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}"
-
+        ontologies:
+          - edam: http://edamontology.org/format_1930
+          - edam: http://edamontology.org/format_3475
+  - suffix:
+      type: string
+      description: The suffix to add to the output file name.
+  - zip_bool:
+      type: boolean
+      description: Whether to gzip the output file.
+      pattern: "true|false"
 output:
   output:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${file_output}:
+          type: file
+          description: Manipulated version of the input sequence file.
+          ontologies: []
+  gz_output:
     - - meta:
           type: map
           description: |
@@ -43,32 +60,31 @@ output:
           type: file
           description: Manipulated and gzipped version of the input sequence file.
           pattern: "*.gz"
-
+          ontologies:
+            - edam: http://edamontology.org/format_3989
   versions_bioawk:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "bioawk":
+      - bioawk:
           type: string
           description: The name of the tool
       - "1.0":
           type: string
-          description: The version of the tool
-
+          description: The expression to obtain the version of the tool
 topics:
   versions:
-    - - "${task.process}":
+    - - ${task.process}:
           type: string
           description: The name of the process
-      - "bioawk":
+      - bioawk:
           type: string
           description: The name of the tool
       - "1.0":
           type: string
-          description: The version of the tool
-
+          description: The expression to obtain the version of the tool
 authors:
   - "@jfy133"
-
 maintainers:
   - "@jfy133"
+schema_version: 1.1.0
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index 270ff1ef3ec9..be0aea9b65dd 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -4,13 +4,13 @@ nextflow_process {
     name "Test Process BIOAWK"
     script "../main.nf"
     process "BIOAWK"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
     tag "bioawk"
 
-    test("test-bioawk") {
+    test("fasta bioawk fasta.gz") {
+        config "./nextflow.config"
 
         when {
             process {
@@ -19,6 +19,33 @@ nextflow_process {
 				    [ id:'test', single_end:false ], // meta map
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
 				]
+				input[1] = "fa"
+				input[2] = true
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fasta bioawk tsv") {
+        config "./nextflow_telomere_check.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file('/lustre/scratch124/tol/teams/tola/users/dp24/nf-modules/modules/nf-core/bioawk/tests/telomere.fasta', checkIfExists: true)
+				]
+				input[1] = "tsv"
+				input[2] = false
 
                 """
             }
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
index fa9b59305fc1..908adbde85a0 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test.snap
+++ b/modules/nf-core/bioawk/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "test-bioawk": {
+    "fasta bioawk fasta.gz": {
         "content": [
             {
                 "0": [
@@ -12,7 +12,17 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,5fe88e58a71f10551df56518c35ba91a"
+                    
+                ],
+                "2": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ],
+                "gz_output": [
+                    
                 ],
                 "output": [
                     [
@@ -23,15 +33,68 @@
                         "sample_1.fa.gz:md5,b558dd15d8940373a032a827d490e693"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,5fe88e58a71f10551df56518c35ba91a"
+                "versions_bioawk": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-25T12:35:30.509942773"
+    },
+    "fasta bioawk tsv": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "telomere_summary.tsv:md5,20facddd524fd8f6c0c03505f0be3e7a"
+                    ]
+                ],
+                "2": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ],
+                "gz_output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "telomere_summary.tsv:md5,20facddd524fd8f6c0c03505f0be3e7a"
+                    ]
+                ],
+                "output": [
+                    
+                ],
+                "versions_bioawk": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-08-28T10:24:46.397249"
+        "timestamp": "2026-03-25T12:39:43.207782527"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
index 5ef017d97353..d8c4757d0ace 100644
--- a/modules/nf-core/bioawk/tests/nextflow.config
+++ b/modules/nf-core/bioawk/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: BIOAWK {
         ext.args = "-c fastx \'{print \">\" \$name ORS length(\$seq)}\'"
-        ext.prefix = "sample_1.fa"
+        ext.prefix = "sample_1"
     }
 }
diff --git a/modules/nf-core/bioawk/tests/nextflow_telomere_check.config b/modules/nf-core/bioawk/tests/nextflow_telomere_check.config
new file mode 100644
index 000000000000..c39bc2889b3d
--- /dev/null
+++ b/modules/nf-core/bioawk/tests/nextflow_telomere_check.config
@@ -0,0 +1,6 @@
+process {
+    withName: BIOAWK {
+        ext.args = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct < 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\t%d\t%.2f\t%s\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s}\'"
+        ext.prefix = "telomere_summary"
+    }
+}

From 84217018313b088b104ccc5c178e62a75953f4ed Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 25 Mar 2026 14:27:39 +0000
Subject: [PATCH 02/15] Updated tests now that dataset is accepted

---
 modules/nf-core/bioawk/tests/main.nf.test     |  2 +-
 .../nf-core/bioawk/tests/main.nf.test.snap    | 28 +++++++++----------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index be0aea9b65dd..4f2d8b54353b 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ], // meta map
-				    file('/lustre/scratch124/tol/teams/tola/users/dp24/nf-modules/modules/nf-core/bioawk/tests/telomere.fasta', checkIfExists: true)
+				    file(params.modules_testdata_base_path + 'generic/telomere/telomeric_motifs.fasta', checkIfExists: true)
 				]
 				input[1] = "tsv"
 				input[2] = false
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
index 908adbde85a0..82756ab54748 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test.snap
+++ b/modules/nf-core/bioawk/tests/main.nf.test.snap
@@ -3,6 +3,9 @@
         "content": [
             {
                 "0": [
+                    
+                ],
+                "1": [
                     [
                         {
                             "id": "test",
@@ -10,9 +13,6 @@
                         },
                         "sample_1.fa.gz:md5,b558dd15d8940373a032a827d490e693"
                     ]
-                ],
-                "1": [
-                    
                 ],
                 "2": [
                     [
@@ -22,9 +22,6 @@
                     ]
                 ],
                 "gz_output": [
-                    
-                ],
-                "output": [
                     [
                         {
                             "id": "test",
@@ -32,6 +29,9 @@
                         },
                         "sample_1.fa.gz:md5,b558dd15d8940373a032a827d490e693"
                     ]
+                ],
+                "output": [
+                    
                 ],
                 "versions_bioawk": [
                     [
@@ -46,15 +46,12 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-25T12:35:30.509942773"
+        "timestamp": "2026-03-25T14:23:36.455899569"
     },
     "fasta bioawk tsv": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     [
                         {
                             "id": "test",
@@ -62,6 +59,9 @@
                         },
                         "telomere_summary.tsv:md5,20facddd524fd8f6c0c03505f0be3e7a"
                     ]
+                ],
+                "1": [
+                    
                 ],
                 "2": [
                     [
@@ -71,6 +71,9 @@
                     ]
                 ],
                 "gz_output": [
+                    
+                ],
+                "output": [
                     [
                         {
                             "id": "test",
@@ -78,9 +81,6 @@
                         },
                         "telomere_summary.tsv:md5,20facddd524fd8f6c0c03505f0be3e7a"
                     ]
-                ],
-                "output": [
-                    
                 ],
                 "versions_bioawk": [
                     [
@@ -95,6 +95,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-25T12:39:43.207782527"
+        "timestamp": "2026-03-25T14:23:43.686125173"
     }
 }
\ No newline at end of file

From 902be18f97b1a98fce5cfa3b79d8182e80dbd5a9 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 25 Mar 2026 20:41:10 +0000
Subject: [PATCH 03/15] Update to bioawk based on review

---
 modules/nf-core/bioawk/main.nf                | 21 +++++----------
 modules/nf-core/bioawk/meta.yml               | 27 ++++++-------------
 modules/nf-core/bioawk/tests/main.nf.test     | 18 ++++++++-----
 .../nf-core/bioawk/tests/main.nf.test.snap    | 18 +++----------
 modules/nf-core/bioawk/tests/nextflow.config  |  4 +--
 .../tests/nextflow_telomere_check.config      |  6 -----
 6 files changed, 32 insertions(+), 62 deletions(-)
 delete mode 100644 modules/nf-core/bioawk/tests/nextflow_telomere_check.config

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 211bf78ffe0d..0ffe5904e542 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -9,12 +9,10 @@ process BIOAWK {
 
     input:
     tuple val(meta), path(input)
-    val suffix
-    val zip_bool
+    val output_file_extension
 
     output:
-    tuple val(meta), path("${file_output}"),    optional: true, emit: output
-    tuple val(meta), path("*.gz"),              optional: true, emit: gz_output
+    tuple val(meta), path("*.${output_file_extension}"), emit: output
     tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions
     // WARN: Version information not provided by tool on CLI. Please update version string above when bumping container versions.
 
@@ -24,19 +22,14 @@ process BIOAWK {
     script:
     def args        = task.ext.args ?: ''
     def prefix      = task.ext.prefix ?: "${meta.id}"
-    file_output     = "${prefix}.${suffix}"
-    if ("${input}" == "${file_output}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate."
+    if ("${input}" == "${prefix}.${output_file_extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate."
 
+    def compress_output = output_file_extension.endsWith(".gz") ? " | gzip " : ""
     """
     bioawk \
-        $args \
-        $input \
-        > ${file_output}
-
-    if [ "${zip_bool}" = "true" ]; then
-        gzip "${file_output}"
-    fi
-
+            $args \
+            $input \
+            ${compress_output} > ${prefix}.${output_file_extension}
     """
 
     stub:
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index 8e3a70df608b..bfc3f9b215d4 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -30,15 +30,16 @@ input:
           Input biological sequence file (optionally gzipped) to be manipulated via the program specified in `$args`.
         pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}"
         ontologies:
-          - edam: http://edamontology.org/format_1930
+          - edam: "http://edamontology.org/format_3003"
+          - edam: "http://edamontology.org/format_3016"
+          - edam: "http://edamontology.org/format_3989"
+          - edam: "http://edamontology.org/format_1975"
+          - edam: "http://edamontology.org/format_1929"
+          - edam: "http://edamontology.org/format_1930"
           - edam: http://edamontology.org/format_3475
-  - suffix:
+  - output_file_extension:
       type: string
       description: The suffix to add to the output file name.
-  - zip_bool:
-      type: boolean
-      description: Whether to gzip the output file.
-      pattern: "true|false"
 output:
   output:
     - - meta:
@@ -46,22 +47,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${file_output}:
+      - "*.${output_file_extension}":
           type: file
           description: Manipulated version of the input sequence file.
           ontologies: []
-  gz_output:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.gz":
-          type: file
-          description: Manipulated and gzipped version of the input sequence file.
-          pattern: "*.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3989
   versions_bioawk:
     - - ${task.process}:
           type: string
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index 4f2d8b54353b..ae3420cdfafa 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -4,6 +4,7 @@ nextflow_process {
     name "Test Process BIOAWK"
     script "../main.nf"
     process "BIOAWK"
+    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -13,15 +14,18 @@ nextflow_process {
         config "./nextflow.config"
 
         when {
+            params {
+                bioawk_command = "-c fastx \'{print \">\" \$name ORS length(\$seq)}\'"
+                bioawk_prefix = "sample_1"
+            }
+
             process {
                 """
                 input[0] = [
 				    [ id:'test', single_end:false ], // meta map
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
 				]
-				input[1] = "fa"
-				input[2] = true
-
+				input[1] = "fa.gz"
                 """
             }
         }
@@ -35,9 +39,13 @@ nextflow_process {
     }
 
     test("fasta bioawk tsv") {
-        config "./nextflow_telomere_check.config"
 
         when {
+            params {
+                bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct < 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\t%d\t%.2f\t%s\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s}\'"
+                bioawk_prefix = "telomere_summary"
+            }
+
             process {
                 """
                 input[0] = [
@@ -45,8 +53,6 @@ nextflow_process {
 				    file(params.modules_testdata_base_path + 'generic/telomere/telomeric_motifs.fasta', checkIfExists: true)
 				]
 				input[1] = "tsv"
-				input[2] = false
-
                 """
             }
         }
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
index 82756ab54748..c4f99a95bf0b 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test.snap
+++ b/modules/nf-core/bioawk/tests/main.nf.test.snap
@@ -3,9 +3,6 @@
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     [
                         {
                             "id": "test",
@@ -14,14 +11,14 @@
                         "sample_1.fa.gz:md5,b558dd15d8940373a032a827d490e693"
                     ]
                 ],
-                "2": [
+                "1": [
                     [
                         "BIOAWK",
                         "bioawk",
                         "1.0"
                     ]
                 ],
-                "gz_output": [
+                "output": [
                     [
                         {
                             "id": "test",
@@ -29,9 +26,6 @@
                         },
                         "sample_1.fa.gz:md5,b558dd15d8940373a032a827d490e693"
                     ]
-                ],
-                "output": [
-                    
                 ],
                 "versions_bioawk": [
                     [
@@ -61,17 +55,11 @@
                     ]
                 ],
                 "1": [
-                    
-                ],
-                "2": [
                     [
                         "BIOAWK",
                         "bioawk",
                         "1.0"
                     ]
-                ],
-                "gz_output": [
-                    
                 ],
                 "output": [
                     [
@@ -97,4 +85,4 @@
         },
         "timestamp": "2026-03-25T14:23:43.686125173"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
index d8c4757d0ace..2ee3ea9d82bb 100644
--- a/modules/nf-core/bioawk/tests/nextflow.config
+++ b/modules/nf-core/bioawk/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: BIOAWK {
-        ext.args = "-c fastx \'{print \">\" \$name ORS length(\$seq)}\'"
-        ext.prefix = "sample_1"
+        ext.args = "${params.bioawk_command}"
+        ext.prefix = "${params.bioawk_prefix}"
     }
 }
diff --git a/modules/nf-core/bioawk/tests/nextflow_telomere_check.config b/modules/nf-core/bioawk/tests/nextflow_telomere_check.config
deleted file mode 100644
index c39bc2889b3d..000000000000
--- a/modules/nf-core/bioawk/tests/nextflow_telomere_check.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-    withName: BIOAWK {
-        ext.args = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct < 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\t%d\t%.2f\t%s\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s}\'"
-        ext.prefix = "telomere_summary"
-    }
-}

From 611d76464b4c3d45a2abf2e6442c2838810aa180 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 25 Mar 2026 20:47:30 +0000
Subject: [PATCH 04/15] Update to bioawk test and snapshot based on review

---
 modules/nf-core/bioawk/tests/main.nf.test      | 2 +-
 modules/nf-core/bioawk/tests/main.nf.test.snap | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index ae3420cdfafa..d0aebb8e2313 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -42,7 +42,7 @@ nextflow_process {
 
         when {
             params {
-                bioawk_command = "-c fastx \'{s = toupper(\$seq); copy_s = s; g = gsub(/G/, \"\", s); pct = 100*g/length(copy_s); rev = (pct < 30); out = rev ? revcomp(\$seq) : \$seq; printf \"%s\t%d\t%.2f\t%s\t%s\\n\", out, g, pct, (rev ? \"true\" : \"false\"), copy_s}\'"
+                bioawk_command = "-c gfastx \'{s = toupper(\$seq); g = gsub(/G/, \"\", s); printf \"%s\\t%d\\n\", s, g}\'"
                 bioawk_prefix = "telomere_summary"
             }
 
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
index c4f99a95bf0b..cc354b1a3ad5 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test.snap
+++ b/modules/nf-core/bioawk/tests/main.nf.test.snap
@@ -51,7 +51,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "telomere_summary.tsv:md5,20facddd524fd8f6c0c03505f0be3e7a"
+                        "telomere_summary.tsv:md5,1d6c6398a229b5005b612f0a393ae6a1"
                     ]
                 ],
                 "1": [
@@ -67,7 +67,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "telomere_summary.tsv:md5,20facddd524fd8f6c0c03505f0be3e7a"
+                        "telomere_summary.tsv:md5,1d6c6398a229b5005b612f0a393ae6a1"
                     ]
                 ],
                 "versions_bioawk": [
@@ -83,6 +83,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-25T14:23:43.686125173"
+        "timestamp": "2026-03-25T20:46:16.217744013"
     }
-}
+}
\ No newline at end of file

From 2b056db98600370e95d66aaefe99dd7d820d063e Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 25 Mar 2026 20:52:06 +0000
Subject: [PATCH 05/15] Linting fix

---
 modules/nf-core/bioawk/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 0ffe5904e542..d99705810393 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -34,7 +34,6 @@ process BIOAWK {
 
     stub:
     """
-    touch ${file_output}
-    echo "" > ${file_output}.gz
+    echo "" > "${prefix}.${output_file_extension}"
     """
 }

From 9d264f86ddc23cc0f61caf7f23a631d7e86b2830 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Wed, 25 Mar 2026 20:55:19 +0000
Subject: [PATCH 06/15] aaaaah prefix

---
 modules/nf-core/bioawk/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index d99705810393..1506fba72faf 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -33,6 +33,7 @@ process BIOAWK {
     """
 
     stub:
+    def prefix      = task.ext.prefix ?: "${meta.id}"
     """
     echo "" > "${prefix}.${output_file_extension}"
     """

From e119506e099446325a066b03797dc016f9c72104 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Thu, 26 Mar 2026 09:53:25 +0000
Subject: [PATCH 07/15] Apply suggestions from code review

Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
---
 modules/nf-core/bioawk/main.nf            |  4 ++--
 modules/nf-core/bioawk/meta.yml           | 14 +++++++-------
 modules/nf-core/bioawk/tests/main.nf.test |  1 -
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 1506fba72faf..1cce5f9a4360 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -13,8 +13,8 @@ process BIOAWK {
 
     output:
     tuple val(meta), path("*.${output_file_extension}"), emit: output
-    tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions
-    // WARN: Version information not provided by tool on CLI. Please update version string above when bumping container versions.
+// WARN: Version information not provided by tool on CLI. Please update version string above when bumping container versions.
+tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index bfc3f9b215d4..a5e55b10dd7f 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -30,13 +30,13 @@ input:
           Input biological sequence file (optionally gzipped) to be manipulated via the program specified in `$args`.
         pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}"
         ontologies:
-          - edam: "http://edamontology.org/format_3003"
-          - edam: "http://edamontology.org/format_3016"
-          - edam: "http://edamontology.org/format_3989"
-          - edam: "http://edamontology.org/format_1975"
-          - edam: "http://edamontology.org/format_1929"
-          - edam: "http://edamontology.org/format_1930"
-          - edam: http://edamontology.org/format_3475
+          - edam: http://edamontology.org/format_3003 # BED
+          - edam: http://edamontology.org/format_3016 # VCF
+          - edam: http://edamontology.org/format_3989 # GZIP
+          - edam: http://edamontology.org/format_1975 # GFF3
+          - edam: http://edamontology.org/format_1929 # FASTA
+          - edam: http://edamontology.org/format_1930 # FASTQ
+          - edam: http://edamontology.org/format_3475 # TSV
   - output_file_extension:
       type: string
       description: The suffix to add to the output file name.
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index d0aebb8e2313..a55c5ff4d97c 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -11,7 +11,6 @@ nextflow_process {
     tag "bioawk"
 
     test("fasta bioawk fasta.gz") {
-        config "./nextflow.config"
 
         when {
             params {

From 93f9c4b8263d7056b1d76470e9cc02d6f207d901 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Thu, 26 Mar 2026 10:02:49 +0000
Subject: [PATCH 08/15] Update modules/nf-core/bioawk/tests/nextflow.config

Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
---
 modules/nf-core/bioawk/tests/nextflow.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
index 2ee3ea9d82bb..84a10f72ffc9 100644
--- a/modules/nf-core/bioawk/tests/nextflow.config
+++ b/modules/nf-core/bioawk/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: BIOAWK {
-        ext.args = "${params.bioawk_command}"
-        ext.prefix = "${params.bioawk_prefix}"
+        ext.args = { "${params.bioawk_command}" }
+        ext.prefix = { "${params.bioawk_prefix}" }
     }
 }

From 834a2f8edfa5cf4448563f931e42ea26f2560ae0 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 26 Mar 2026 10:13:56 +0000
Subject: [PATCH 09/15] SPELLING MISTAKE

---
 modules/nf-core/bioawk/main.nf                 | 10 +++++-----
 modules/nf-core/bioawk/tests/main.nf.test      |  2 +-
 modules/nf-core/bioawk/tests/main.nf.test.snap |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 1cce5f9a4360..503701b6905c 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -13,8 +13,8 @@ process BIOAWK {
 
     output:
     tuple val(meta), path("*.${output_file_extension}"), emit: output
-// WARN: Version information not provided by tool on CLI. Please update version string above when bumping container versions.
-tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions
+    // WARN: Version information not provided by tool on CLI. Please update version string above when bumping container versions.
+    tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,9 +26,9 @@ tuple val("${task.process}"), val('bioawk'), val("1.0"), emit: versions_bioawk,
 
     def compress_output = output_file_extension.endsWith(".gz") ? " | gzip " : ""
     """
-    bioawk \
-            $args \
-            $input \
+    bioawk \\
+            $args \\
+            $input \\
             ${compress_output} > ${prefix}.${output_file_extension}
     """
 
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index a55c5ff4d97c..d85a20cb5111 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -41,7 +41,7 @@ nextflow_process {
 
         when {
             params {
-                bioawk_command = "-c gfastx \'{s = toupper(\$seq); g = gsub(/G/, \"\", s); printf \"%s\\t%d\\n\", s, g}\'"
+                bioawk_command = "-c fastx \'{s = toupper(\$seq); g = gsub(/G/, \"\", s); printf \"%s\\t%d\\n\", s, g}\'"
                 bioawk_prefix = "telomere_summary"
             }
 
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
index cc354b1a3ad5..c02a080d7edd 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test.snap
+++ b/modules/nf-core/bioawk/tests/main.nf.test.snap
@@ -83,6 +83,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-25T20:46:16.217744013"
+        "timestamp": "2026-03-26T10:13:18.610496559"
     }
 }
\ No newline at end of file

From 7f67682ee1968bd9712287ff2b68dd37d0990ad5 Mon Sep 17 00:00:00 2001
From: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com>
Date: Thu, 26 Mar 2026 10:25:35 +0000
Subject: [PATCH 10/15] Update modules/nf-core/bioawk/main.nf

Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
---
 modules/nf-core/bioawk/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 503701b6905c..893dfb626452 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -34,7 +34,8 @@ process BIOAWK {
 
     stub:
     def prefix      = task.ext.prefix ?: "${meta.id}"
+    def compress_output = output_file_extension.endsWith(".gz") ? " | gzip " : ""
     """
-    echo "" > "${prefix}.${output_file_extension}"
+    echo "" ${compress_output} > "${prefix}.${output_file_extension}"
     """
 }

From 63c5ad299bf86242efd98935b8bc91669bef76b2 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 26 Mar 2026 16:40:11 +0000
Subject: [PATCH 11/15] Update bioawk based on discussions

---
 modules/nf-core/bioawk/main.nf               | 22 ++++++++++++++------
 modules/nf-core/bioawk/meta.yml              | 17 +++++++++++++++
 modules/nf-core/bioawk/tests/main.nf.test    | 14 +++++++++----
 modules/nf-core/bioawk/tests/nextflow.config |  2 +-
 4 files changed, 44 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 893dfb626452..e3a919acad9d 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -9,6 +9,9 @@ process BIOAWK {
 
     input:
     tuple val(meta), path(input)
+    path(program_file)
+    val(disable_redirect_output)
+    val bioawk_extension
     val output_file_extension
 
     output:
@@ -21,21 +24,28 @@ process BIOAWK {
 
     script:
     def args        = task.ext.args ?: ''
+    def args2       = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given
+    program         = program_file ? "-f ${program_file}" : "${args2}"
+    awk_ext         = bioawk_extension ? "-c ${bioawk_extension}" : ""
     def prefix      = task.ext.prefix ?: "${meta.id}"
+    output_cmd      = output_file_extension.endsWith("gz") ? "| gzip > ${prefix}.${output_file_extension}" : "> ${prefix}.${output_file_extension}"
+    output          = disable_redirect_output ? "" : output_cmd
+
     if ("${input}" == "${prefix}.${output_file_extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate."
 
-    def compress_output = output_file_extension.endsWith(".gz") ? " | gzip " : ""
     """
     bioawk \\
-            $args \\
-            $input \\
-            ${compress_output} > ${prefix}.${output_file_extension}
+            ${awk_ext} \\
+            ${args} \\
+            ${program} \\
+            ${input} \\
+            ${output}
     """
 
     stub:
     def prefix      = task.ext.prefix ?: "${meta.id}"
-    def compress_output = output_file_extension.endsWith(".gz") ? " | gzip " : ""
+    def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch"
     """
-    echo "" ${compress_output} > "${prefix}.${output_file_extension}"
+    ${create_cmd} ${prefix}.${output_file_extension}
     """
 }
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index a5e55b10dd7f..df87ab069157 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -37,6 +37,23 @@ input:
           - edam: http://edamontology.org/format_1929 # FASTA
           - edam: http://edamontology.org/format_1930 # FASTQ
           - edam: http://edamontology.org/format_3475 # TSV
+  - program_file:
+      type: file
+      description: Optional file containing logic for awk to execute. If you don't
+        wish to use a file, you can use `ext.args2` to specify the logic.
+      pattern: "*"
+      ontologies: []
+  - disable_redirect_output:
+      type: boolean
+      description: |
+        Disable the redirection of awk output to a given file. This is
+        useful if you want to use awk's built-in redirect to write files instead
+        of the shell's redirect.
+  - bioawk_extension:
+      type: string
+      description: |
+        The extension to use for the bioawk program.
+        enum: ["fastx", "bed", "vcf", "sam"]
   - output_file_extension:
       type: string
       description: The suffix to add to the output file name.
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index d85a20cb5111..0756fad4e2a3 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -14,7 +14,7 @@ nextflow_process {
 
         when {
             params {
-                bioawk_command = "-c fastx \'{print \">\" \$name ORS length(\$seq)}\'"
+                bioawk_command = "\'{print \">\" \$name ORS length(\$seq)}\'"
                 bioawk_prefix = "sample_1"
             }
 
@@ -24,7 +24,10 @@ nextflow_process {
 				    [ id:'test', single_end:false ], // meta map
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
 				]
-				input[1] = "fa.gz"
+				input[1] = []
+				input[2] = false
+				input[3] = "fastx"
+				input[4] = "fa.gz"
                 """
             }
         }
@@ -41,7 +44,7 @@ nextflow_process {
 
         when {
             params {
-                bioawk_command = "-c fastx \'{s = toupper(\$seq); g = gsub(/G/, \"\", s); printf \"%s\\t%d\\n\", s, g}\'"
+                bioawk_command = "\'{s = toupper(\$seq); g = gsub(/G/, \"\", s); printf \"%s\\t%d\\n\", s, g}\'"
                 bioawk_prefix = "telomere_summary"
             }
 
@@ -51,7 +54,10 @@ nextflow_process {
 				    [ id:'test', single_end:false ], // meta map
 				    file(params.modules_testdata_base_path + 'generic/telomere/telomeric_motifs.fasta', checkIfExists: true)
 				]
-				input[1] = "tsv"
+				input[1] = []
+				input[2] = false
+				input[3] = "fastx"
+				input[4] = "tsv"
                 """
             }
         }
diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
index 84a10f72ffc9..4e8bf47c0139 100644
--- a/modules/nf-core/bioawk/tests/nextflow.config
+++ b/modules/nf-core/bioawk/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: BIOAWK {
-        ext.args = { "${params.bioawk_command}" }
+        ext.args2 = { "${params.bioawk_command}" }
         ext.prefix = { "${params.bioawk_prefix}" }
     }
 }

From b6e1b146496c3e3b1fe021d3972a0481d39d8a90 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 26 Mar 2026 16:47:25 +0000
Subject: [PATCH 12/15] Missed a suffix

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

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 8781be1da1c1..6a8819be67f0 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -45,7 +45,7 @@ process BIOAWK {
 
     stub:
     def prefix     = task.ext.prefix ?: "${meta.id}"
-    def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch"
+    def create_cmd = output_file_extension.endsWith("gz") ? "echo '' | gzip >" : "touch"
     """
     ${create_cmd} ${prefix}.${output_file_extension}
     """

From 2fe9865baa127ff3f1e50550f06f1c74a93974e6 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Thu, 26 Mar 2026 19:58:06 +0000
Subject: [PATCH 13/15] Update for programs and tests

---
 modules/nf-core/bioawk/main.nf                |  4 +-
 modules/nf-core/bioawk/meta.yml               |  3 +-
 modules/nf-core/bioawk/tests/main.nf.test     | 60 +++++++++++-
 .../nf-core/bioawk/tests/main.nf.test.snap    | 94 ++++++++++++++++++-
 modules/nf-core/bioawk/tests/nextflow.config  |  2 +-
 5 files changed, 153 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 6a8819be67f0..52d296595fb5 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -24,8 +24,7 @@ process BIOAWK {
 
     script:
     def args        = task.ext.args ?: ''
-    def args2       = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given
-    program         = program_file ? "-f ${program_file}" : "${args2}"
+    program         = program_file ? "-f ${program_file}" : "${args}"
     awk_ext         = bioawk_extension ? "-c ${bioawk_extension}" : ""
     def prefix      = task.ext.prefix ?: "${meta.id}"
     output_cmd      = output_file_extension.endsWith("gz") ? "| gzip > ${prefix}.${output_file_extension}" : "> ${prefix}.${output_file_extension}"
@@ -37,7 +36,6 @@ process BIOAWK {
     """
     bioawk \\
             ${awk_ext} \\
-            ${args} \\
             ${program} \\
             ${input} \\
             ${output}
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index df87ab069157..6c1fda39b6d5 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -42,7 +42,8 @@ input:
       description: Optional file containing logic for awk to execute. If you don't
         wish to use a file, you can use `ext.args2` to specify the logic.
       pattern: "*"
-      ontologies: []
+      ontologies:
+        - edam: http://edamontology.org/data_3671 # TXT
   - disable_redirect_output:
       type: boolean
       description: |
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index 0756fad4e2a3..092e37b45868 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -44,7 +44,7 @@ nextflow_process {
 
         when {
             params {
-                bioawk_command = "\'{s = toupper(\$seq); g = gsub(/G/, \"\", s); printf \"%s\\t%d\\n\", s, g}\'"
+                bioawk_command = "\'BEGIN {OFS = \'\\t\'} {print toupper(\$seq), gsub(/G/, \"\", \$seq)} \'"
                 bioawk_prefix = "telomere_summary"
             }
 
@@ -70,4 +70,62 @@ nextflow_process {
         }
     }
 
+    test("fasta bioawk tsv - no redirect") {
+
+        when {
+            params {
+                bioawk_prefix = "telomere_summary"
+            }
+
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'generic/telomere/telomeric_motifs.fasta', checkIfExists: true)
+				]
+				input[1] = channel.of('BEGIN {OFS = "\t"} {print toupper(\$seq), gsub(/G/, "", \$seq) > "output.tsv"}').collectFile(name:"program.awk")
+				input[2] = true
+				input[3] = "fastx"
+				input[4] = "tsv"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("fasta bioawk tsv - program file") {
+
+        when {
+            params {
+                bioawk_prefix = "telomere_summary"
+            }
+
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'generic/telomere/telomeric_motifs.fasta', checkIfExists: true)
+				]
+				input[1] = channel.of('BEGIN {OFS = "\t"} {print toupper(\$seq), gsub(/G/, "", \$seq) }').collectFile(name:"program.awk")
+				input[2] = false
+				input[3] = "fastx"
+				input[4] = "tsv"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/bioawk/tests/main.nf.test.snap b/modules/nf-core/bioawk/tests/main.nf.test.snap
index c02a080d7edd..e938fbfc318f 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test.snap
+++ b/modules/nf-core/bioawk/tests/main.nf.test.snap
@@ -1,4 +1,47 @@
 {
+    "fasta bioawk tsv - no redirect": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "output.tsv:md5,45a26fc19df7fafe489fb66ee057b069"
+                    ]
+                ],
+                "1": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "output.tsv:md5,45a26fc19df7fafe489fb66ee057b069"
+                    ]
+                ],
+                "versions_bioawk": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-26T17:25:23.91735062"
+    },
     "fasta bioawk fasta.gz": {
         "content": [
             {
@@ -40,7 +83,50 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-25T14:23:36.455899569"
+        "timestamp": "2026-03-26T19:57:03.10201788"
+    },
+    "fasta bioawk tsv - program file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "telomere_summary.tsv:md5,45a26fc19df7fafe489fb66ee057b069"
+                    ]
+                ],
+                "1": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "telomere_summary.tsv:md5,45a26fc19df7fafe489fb66ee057b069"
+                    ]
+                ],
+                "versions_bioawk": [
+                    [
+                        "BIOAWK",
+                        "bioawk",
+                        "1.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-03-26T17:25:31.418710838"
     },
     "fasta bioawk tsv": {
         "content": [
@@ -51,7 +137,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "telomere_summary.tsv:md5,1d6c6398a229b5005b612f0a393ae6a1"
+                        "telomere_summary.tsv:md5,45a26fc19df7fafe489fb66ee057b069"
                     ]
                 ],
                 "1": [
@@ -67,7 +153,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "telomere_summary.tsv:md5,1d6c6398a229b5005b612f0a393ae6a1"
+                        "telomere_summary.tsv:md5,45a26fc19df7fafe489fb66ee057b069"
                     ]
                 ],
                 "versions_bioawk": [
@@ -83,6 +169,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-03-26T10:13:18.610496559"
+        "timestamp": "2026-03-26T19:57:10.200126559"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
index 4e8bf47c0139..84a10f72ffc9 100644
--- a/modules/nf-core/bioawk/tests/nextflow.config
+++ b/modules/nf-core/bioawk/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: BIOAWK {
-        ext.args2 = { "${params.bioawk_command}" }
+        ext.args = { "${params.bioawk_command}" }
         ext.prefix = { "${params.bioawk_prefix}" }
     }
 }

From 4c640760c2dffba113ffa1bfbcfb8ef86111e810 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Mon, 30 Mar 2026 12:21:12 +0100
Subject: [PATCH 14/15] Update to use args for -c

---
 modules/nf-core/bioawk/main.nf               |  6 ++----
 modules/nf-core/bioawk/meta.yml              |  5 -----
 modules/nf-core/bioawk/tests/main.nf.test    | 16 ++++++++--------
 modules/nf-core/bioawk/tests/nextflow.config |  3 ++-
 4 files changed, 12 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index 52d296595fb5..db6f86606c9e 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -11,7 +11,6 @@ process BIOAWK {
     tuple val(meta), path(input)
     path(program_file)
     val(disable_redirect_output)
-    val bioawk_extension
     val output_file_extension
 
     output:
@@ -24,8 +23,7 @@ process BIOAWK {
 
     script:
     def args        = task.ext.args ?: ''
-    program         = program_file ? "-f ${program_file}" : "${args}"
-    awk_ext         = bioawk_extension ? "-c ${bioawk_extension}" : ""
+    program         = program_file ? "-f ${program_file}" : "${args2}"
     def prefix      = task.ext.prefix ?: "${meta.id}"
     output_cmd      = output_file_extension.endsWith("gz") ? "| gzip > ${prefix}.${output_file_extension}" : "> ${prefix}.${output_file_extension}"
     output          = disable_redirect_output ? "" : output_cmd
@@ -35,7 +33,7 @@ process BIOAWK {
     def compress_output = output_file_extension.endsWith(".gz") ? " | gzip " : ""
     """
     bioawk \\
-            ${awk_ext} \\
+            ${args} \\
             ${program} \\
             ${input} \\
             ${output}
diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml
index 6c1fda39b6d5..7281e0b07073 100644
--- a/modules/nf-core/bioawk/meta.yml
+++ b/modules/nf-core/bioawk/meta.yml
@@ -50,11 +50,6 @@ input:
         Disable the redirection of awk output to a given file. This is
         useful if you want to use awk's built-in redirect to write files instead
         of the shell's redirect.
-  - bioawk_extension:
-      type: string
-      description: |
-        The extension to use for the bioawk program.
-        enum: ["fastx", "bed", "vcf", "sam"]
   - output_file_extension:
       type: string
       description: The suffix to add to the output file name.
diff --git a/modules/nf-core/bioawk/tests/main.nf.test b/modules/nf-core/bioawk/tests/main.nf.test
index 092e37b45868..7ab40884cb01 100644
--- a/modules/nf-core/bioawk/tests/main.nf.test
+++ b/modules/nf-core/bioawk/tests/main.nf.test
@@ -14,6 +14,7 @@ nextflow_process {
 
         when {
             params {
+                bioawk_extension = "-c fastx"
                 bioawk_command = "\'{print \">\" \$name ORS length(\$seq)}\'"
                 bioawk_prefix = "sample_1"
             }
@@ -26,8 +27,7 @@ nextflow_process {
 				]
 				input[1] = []
 				input[2] = false
-				input[3] = "fastx"
-				input[4] = "fa.gz"
+				input[3] = "fa.gz"
                 """
             }
         }
@@ -44,6 +44,7 @@ nextflow_process {
 
         when {
             params {
+                bioawk_extension = "-c fastx"
                 bioawk_command = "\'BEGIN {OFS = \'\\t\'} {print toupper(\$seq), gsub(/G/, \"\", \$seq)} \'"
                 bioawk_prefix = "telomere_summary"
             }
@@ -56,8 +57,7 @@ nextflow_process {
 				]
 				input[1] = []
 				input[2] = false
-				input[3] = "fastx"
-				input[4] = "tsv"
+				input[3] = "tsv"
                 """
             }
         }
@@ -74,6 +74,7 @@ nextflow_process {
 
         when {
             params {
+                bioawk_extension = "-c fastx"
                 bioawk_prefix = "telomere_summary"
             }
 
@@ -85,8 +86,7 @@ nextflow_process {
 				]
 				input[1] = channel.of('BEGIN {OFS = "\t"} {print toupper(\$seq), gsub(/G/, "", \$seq) > "output.tsv"}').collectFile(name:"program.awk")
 				input[2] = true
-				input[3] = "fastx"
-				input[4] = "tsv"
+				input[3] = "tsv"
                 """
             }
         }
@@ -103,6 +103,7 @@ nextflow_process {
 
         when {
             params {
+                bioawk_extension = "-c fastx"
                 bioawk_prefix = "telomere_summary"
             }
 
@@ -114,8 +115,7 @@ nextflow_process {
 				]
 				input[1] = channel.of('BEGIN {OFS = "\t"} {print toupper(\$seq), gsub(/G/, "", \$seq) }').collectFile(name:"program.awk")
 				input[2] = false
-				input[3] = "fastx"
-				input[4] = "tsv"
+				input[3] = "tsv"
                 """
             }
         }
diff --git a/modules/nf-core/bioawk/tests/nextflow.config b/modules/nf-core/bioawk/tests/nextflow.config
index 84a10f72ffc9..487101e1932e 100644
--- a/modules/nf-core/bioawk/tests/nextflow.config
+++ b/modules/nf-core/bioawk/tests/nextflow.config
@@ -1,6 +1,7 @@
 process {
     withName: BIOAWK {
-        ext.args = { "${params.bioawk_command}" }
+        ext.args = { "${params.bioawk_extension}" }
+        ext.args2 = { "${params.bioawk_command}" }
         ext.prefix = { "${params.bioawk_prefix}" }
     }
 }

From a944e1ab3392fda5eb77a3d51b251873e8eca1d5 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Mon, 30 Mar 2026 13:01:46 +0100
Subject: [PATCH 15/15] Didn't add in args2 again

---
 modules/nf-core/bioawk/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf
index db6f86606c9e..4eaf195c1084 100644
--- a/modules/nf-core/bioawk/main.nf
+++ b/modules/nf-core/bioawk/main.nf
@@ -23,6 +23,7 @@ process BIOAWK {
 
     script:
     def args        = task.ext.args ?: ''
+    def args2       = task.ext.args2 ?: ''
     program         = program_file ? "-f ${program_file}" : "${args2}"
     def prefix      = task.ext.prefix ?: "${meta.id}"
     output_cmd      = output_file_extension.endsWith("gz") ? "| gzip > ${prefix}.${output_file_extension}" : "> ${prefix}.${output_file_extension}"