From 75f95ec19656cd274db05f71e7942a40d15d64a7 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 11:24:45 +1100
Subject: [PATCH 01/18] rgi/bwt: add draft

  - Use template from rgi/main
---
 modules/nf-core/rgi/bwt/environment.yml    |  7 ++
 modules/nf-core/rgi/bwt/main.nf            | 89 +++++++++++++++++++
 modules/nf-core/rgi/bwt/meta.yml           | 99 ++++++++++++++++++++++
 modules/nf-core/rgi/bwt/tests/main.nf.test | 94 ++++++++++++++++++++
 4 files changed, 289 insertions(+)
 create mode 100644 modules/nf-core/rgi/bwt/environment.yml
 create mode 100644 modules/nf-core/rgi/bwt/main.nf
 create mode 100644 modules/nf-core/rgi/bwt/meta.yml
 create mode 100644 modules/nf-core/rgi/bwt/tests/main.nf.test

diff --git a/modules/nf-core/rgi/bwt/environment.yml b/modules/nf-core/rgi/bwt/environment.yml
new file mode 100644
index 000000000000..b6b2d3438158
--- /dev/null
+++ b/modules/nf-core/rgi/bwt/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::rgi=6.0.5
diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
new file mode 100644
index 000000000000..70b5bd6c3eae
--- /dev/null
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -0,0 +1,89 @@
+process RGI_BWT {
+    tag "${meta.id}"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/rgi:6.0.5--pyh05cac1d_0'
+        : 'biocontainers/rgi:6.0.5--pyh05cac1d_0'}"
+
+    input:
+    tuple val(meta), path(fasta)
+    path card
+    path wildcard
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.txt"), emit: tsv
+    tuple val(meta), path("temp/"), emit: tmp
+    env RGI_VERSION, emit: tool_version
+    env DB_VERSION, emit: db_version
+    path "versions.yml", emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    // This customizes the command: rgi bwt
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def load_wildcard = ""
+
+    if (wildcard) {
+        load_wildcard = """ \\
+            --wildcard_annotation ${wildcard}/wildcard_database_v\$DB_VERSION.fasta \\
+            --wildcard_annotation_all_models ${wildcard}/wildcard_database_v\$DB_VERSION\\_all.fasta \\
+            --wildcard_index ${wildcard}/wildcard/index-for-model-sequences.txt \\
+            --amr_kmers ${wildcard}/wildcard/all_amr_61mers.txt \\
+            --kmer_database ${wildcard}/wildcard/61_kmer_db.json \\
+            --kmer_size 61
+        """
+    }
+
+    """
+    DB_VERSION=\$(ls ${card}/card_database_*_all.fasta | sed "s/${card}\\/card_database_v\\([0-9].*[0-9]\\).*/\\1/")
+
+    rgi \\
+        load \\
+        ${args} \\
+        --card_json ${card}/card.json \\
+        --debug --local \\
+        --card_annotation ${card}/card_database_v\$DB_VERSION.fasta \\
+        --card_annotation_all_models ${card}/card_database_v\$DB_VERSION\\_all.fasta \\
+        ${load_wildcard}
+
+    rgi \\
+        bwt \\
+        ${args} \\
+        --threads ${task.cpus} \\
+        --output_file ${prefix} \\
+        --input_sequence ${fasta}
+
+    mkdir temp/
+    for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e \$FILE ]] && mv \$FILE temp/; done
+
+    RGI_VERSION=\$(rgi main --version)
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(echo \$RGI_VERSION)
+        rgi-database: \$(echo \$DB_VERSION)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir -p temp
+    touch test.json
+    touch test.txt
+
+    RGI_VERSION=\$(rgi main --version)
+    DB_VERSION=stub_version
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(echo \$RGI_VERSION)
+        rgi-database: \$(echo \$DB_VERSION)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
new file mode 100644
index 000000000000..ff5436c13398
--- /dev/null
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -0,0 +1,99 @@
+name: rgi_bwt
+description: Predict antibiotic resistance from protein or nucleotide data
+keywords:
+  - bacteria
+  - fasta
+  - antibiotic resistance
+tools:
+  - rgi:
+      description: This tool provides a preliminary annotation of your DNA sequence(s)
+        based upon the data available in The Comprehensive Antibiotic Resistance Database
+        (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will
+        be highlighted. As CARD expands to include more pathogens, genomes, plasmids,
+        and ontology terms this tool will grow increasingly powerful in providing first-pass
+        detection of antibiotic resistance associated genes. See license at CARD website
+      homepage: https://card.mcmaster.ca
+      documentation: https://github.com/arpcard/rgi
+      tool_dev_url: https://github.com/arpcard/rgi
+      doi: "10.1093/nar/gkz935"
+      licence: ["https://card.mcmaster.ca/about"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Nucleotide or protein sequences in FASTA format
+        pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+        ontologies: []
+  - card:
+      type: directory
+      description: Directory containing the CARD database. This is expected to be the
+        unarchived but otherwise unaltered download folder (see RGI documentation for
+        download instructions).
+      pattern: "*/"
+  - wildcard:
+      type: directory
+      description: Directory containing the WildCARD database (optional). This is expected
+        to be the unarchived but otherwise unaltered download folder (see RGI documentation
+        for download instructions).
+      pattern: "*/"
+output:
+  json:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.json":
+          type: file
+          description: JSON formatted file with RGI results
+          pattern: "*.{json}"
+          ontologies:
+            - edam: http://edamontology.org/format_3464 # JSON
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.txt":
+          type: file
+          description: Tab-delimited file with RGI results
+          pattern: "*.{txt}"
+          ontologies: []
+  tmp:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - temp/:
+          type: directory
+          description: Directory containing various intermediate files
+          pattern: "temp/"
+  tool_version:
+    - RGI_VERSION:
+        type: string
+        description: The version of the tool in string format (useful for downstream
+          tools such as hAMRronization)
+  db_version:
+    - DB_VERSION:
+        type: string
+        description: The version of the used database in string format (useful for downstream
+          tools such as hAMRronization)
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@vinisalazar"
+maintainers:
+  - "@nickp60"
+  - "@vinisalazar"
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test b/modules/nf-core/rgi/bwt/tests/main.nf.test
new file mode 100644
index 000000000000..7138e09841ee
--- /dev/null
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test
@@ -0,0 +1,94 @@
+nextflow_process {
+
+    name "Test Process RGI_BWT"
+    script "../main.nf"
+    process "RGI_BWT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rgi"
+    tag "rgi/bwt"
+    tag "rgi/cardannotation"
+    tag "untar"
+
+    setup {
+        run("UNTAR") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+            """
+            file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('card-data.tar.bz2')
+
+            input[0] = [
+                [ ],
+                file("card-data.tar.bz2")
+            ]
+            """
+            }
+        }
+
+        run("RGI_CARDANNOTATION") {
+            script "modules/nf-core/rgi/cardannotation"
+            process {
+                """
+                input[0] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+    }
+
+
+    test("rgi/bwt - haemophilus_influenzae - genome_fna_gz") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+                ]
+                input[1] = RGI_CARDANNOTATION.out.db
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.tsv,
+                    process.out.json,
+                    file(process.out.tmp.get(0).get(1)).list().sort(),
+                    process.out.tool_version,
+                    process.out.db_version,
+                    ).match() }
+            )
+        }
+    }
+
+    test("rgi/bwt - haemophilus_influenzae - genome_fna_gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+                ]
+                input[1] = RGI_CARDANNOTATION.out.db
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

From 42bf5c7e7140637a3ac69417100500dd4358357b Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 11:54:03 +1100
Subject: [PATCH 02/18] rgi/bwt: editing input channel

  - Use fastq pair instead of single fasta file
---
 modules/nf-core/rgi/bwt/main.nf            |  8 ++++++--
 modules/nf-core/rgi/bwt/tests/main.nf.test | 10 ++++++----
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 70b5bd6c3eae..9d31ea47acae 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -8,7 +8,7 @@ process RGI_BWT {
         : 'biocontainers/rgi:6.0.5--pyh05cac1d_0'}"
 
     input:
-    tuple val(meta), path(fasta)
+    tuple val(meta), path(reads)
     path card
     path wildcard
 
@@ -27,6 +27,8 @@ process RGI_BWT {
     def args = task.ext.args ?: ''
     // This customizes the command: rgi bwt
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def read_one = reads instanceof List ? reads[0] : reads
+    def read_two = reads instanceof List && reads.size() > 1 ? reads[1] : null
     def load_wildcard = ""
 
     if (wildcard) {
@@ -57,7 +59,9 @@ process RGI_BWT {
         ${args} \\
         --threads ${task.cpus} \\
         --output_file ${prefix} \\
-        --input_sequence ${fasta}
+        --read_one ${read_one} \\
+        ${ read_two ? "--read_two ${read_two}" : "" }
+
 
     mkdir temp/
     for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e \$FILE ]] && mv \$FILE temp/; done
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test b/modules/nf-core/rgi/bwt/tests/main.nf.test
index 7138e09841ee..075df33db1bb 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test
@@ -37,14 +37,15 @@ nextflow_process {
     }
 
 
-    test("rgi/bwt - haemophilus_influenzae - genome_fna_gz") {
+    test("rgi/bwt - homo_sapiens - test_fastq_gz") {
 
         when {
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+                    file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true),
                 ]
                 input[1] = RGI_CARDANNOTATION.out.db
                 input[2] = []
@@ -67,7 +68,7 @@ nextflow_process {
         }
     }
 
-    test("rgi/bwt - haemophilus_influenzae - genome_fna_gz - stub") {
+    test("rgi/bwt - homo_sapiens - test_fastq_gz - stub") {
 
         options "-stub"
 
@@ -76,7 +77,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true)
+                    file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true),
                 ]
                 input[1] = RGI_CARDANNOTATION.out.db
                 input[2] = []

From 77ec4ba074c587491c07a5c0285152e16013b5be Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 12:33:42 +1100
Subject: [PATCH 03/18] rgi/bwt: edit meta.yaml

  - add fastq extensions to 'pattern'
---
 modules/nf-core/rgi/bwt/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
index ff5436c13398..8bffe3e1e10d 100644
--- a/modules/nf-core/rgi/bwt/meta.yml
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -26,8 +26,8 @@ input:
           e.g. [ id:'test', single_end:false ]
     - fasta:
         type: file
-        description: Nucleotide or protein sequences in FASTA format
-        pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+        description: Nucleotide sequences in FASTQ or FASTA format
+        pattern: "*.{fastq,fastq.gz,fq,fq.gz,fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
         ontologies: []
   - card:
       type: directory

From fe0039c4d21eb29542701746e1275bba32724e87 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 13:40:46 +1100
Subject: [PATCH 04/18] rgi/bwt: update meta.yaml

  - Trying to pass linter
---
 modules/nf-core/rgi/bwt/meta.yml | 35 ++++++++++++++++----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
index 8bffe3e1e10d..43210e91d392 100644
--- a/modules/nf-core/rgi/bwt/meta.yml
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -6,12 +6,13 @@ keywords:
   - antibiotic resistance
 tools:
   - rgi:
-      description: This tool provides a preliminary annotation of your DNA sequence(s)
-        based upon the data available in The Comprehensive Antibiotic Resistance Database
-        (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will
-        be highlighted. As CARD expands to include more pathogens, genomes, plasmids,
-        and ontology terms this tool will grow increasingly powerful in providing first-pass
-        detection of antibiotic resistance associated genes. See license at CARD website
+      description: This tool provides a preliminary annotation of your DNA
+        sequence(s) based upon the data available in The Comprehensive Antibiotic
+        Resistance Database (CARD). Hits to genes tagged with Antibiotic
+        Resistance ontology terms will be highlighted. As CARD expands to include
+        more pathogens, genomes, plasmids, and ontology terms this tool will grow
+        increasingly powerful in providing first-pass detection of antibiotic
+        resistance associated genes. See license at CARD website.
       homepage: https://card.mcmaster.ca
       documentation: https://github.com/arpcard/rgi
       tool_dev_url: https://github.com/arpcard/rgi
@@ -24,22 +25,22 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - fasta:
+    - reads:
         type: file
         description: Nucleotide sequences in FASTQ or FASTA format
         pattern: "*.{fastq,fastq.gz,fq,fq.gz,fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
         ontologies: []
   - card:
       type: directory
-      description: Directory containing the CARD database. This is expected to be the
-        unarchived but otherwise unaltered download folder (see RGI documentation for
-        download instructions).
+      description: Directory containing the CARD database. This is expected to be
+        the unarchived but otherwise unaltered download folder (see RGI
+        documentation for download instructions).
       pattern: "*/"
   - wildcard:
       type: directory
-      description: Directory containing the WildCARD database (optional). This is expected
-        to be the unarchived but otherwise unaltered download folder (see RGI documentation
-        for download instructions).
+      description: Directory containing the WildCARD database (optional). This is
+        expected to be the unarchived but otherwise unaltered download folder (see
+        RGI documentation for download instructions).
       pattern: "*/"
 output:
   json:
@@ -78,13 +79,13 @@ output:
   tool_version:
     - RGI_VERSION:
         type: string
-        description: The version of the tool in string format (useful for downstream
-          tools such as hAMRronization)
+        description: The version of the tool in string format (useful for
+          downstream tools such as hAMRronization)
   db_version:
     - DB_VERSION:
         type: string
-        description: The version of the used database in string format (useful for downstream
-          tools such as hAMRronization)
+        description: The version of the used database in string format (useful for
+          downstream tools such as hAMRronization)
   versions:
     - versions.yml:
         type: file

From 6252f12d48570aae7c0e6983889049707136c4ec Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 13:54:17 +1100
Subject: [PATCH 05/18] rgi/bwt: add test snapshot

---
 .../nf-core/rgi/bwt/tests/main.nf.test.snap   | 89 +++++++++++++++++++
 1 file changed, 89 insertions(+)
 create mode 100644 modules/nf-core/rgi/bwt/tests/main.nf.test.snap

diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
new file mode 100644
index 000000000000..1dbec1d9b0fe
--- /dev/null
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -0,0 +1,89 @@
+{
+    "rgi/bwt - homo_sapiens - test_fastq_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "3": [
+                    "6.0.5"
+                ],
+                "4": [
+                    "stub_version"
+                ],
+                "5": [
+                    "versions.yml:md5,47cb67c7969fe73d5f59c5fee0cda9c6"
+                ],
+                "db_version": [
+                    "stub_version"
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tmp": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "tool_version": [
+                    "6.0.5"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,47cb67c7969fe73d5f59c5fee0cda9c6"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-18T13:42:37.634355"
+    }
+}
\ No newline at end of file

From 738ffc34637d281a3498b4f6eb4b8445512ede42 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 15:35:00 +1100
Subject: [PATCH 06/18] rgi/bwt: add '--local' flag

  - build KMA/BWT index in workdir instead of program executable dir
  - update test snapshot
---
 modules/nf-core/rgi/bwt/main.nf               | 10 +++-
 .../nf-core/rgi/bwt/tests/main.nf.test.snap   | 52 ++++++++++++++++++-
 2 files changed, 60 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 9d31ea47acae..f77ed7700ae6 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -25,6 +25,12 @@ process RGI_BWT {
 
     script:
     def args = task.ext.args ?: ''
+    def use_local = task.ext.local == null ? true : task.ext.local as boolean
+    // Add this to nextflow.config if not using local:
+    // withName: RGI_BWT {
+    //      ext.local = false
+    //  }
+    def local_flag = use_local ? '--local' : ''
     // This customizes the command: rgi bwt
     def prefix = task.ext.prefix ?: "${meta.id}"
     def read_one = reads instanceof List ? reads[0] : reads
@@ -48,8 +54,9 @@ process RGI_BWT {
     rgi \\
         load \\
         ${args} \\
+        ${local_flag} \\
         --card_json ${card}/card.json \\
-        --debug --local \\
+        --debug \\
         --card_annotation ${card}/card_database_v\$DB_VERSION.fasta \\
         --card_annotation_all_models ${card}/card_database_v\$DB_VERSION\\_all.fasta \\
         ${load_wildcard}
@@ -57,6 +64,7 @@ process RGI_BWT {
     rgi \\
         bwt \\
         ${args} \\
+        ${local_flag} \\
         --threads ${task.cpus} \\
         --output_file ${prefix} \\
         --read_one ${read_one} \\
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
index 1dbec1d9b0fe..351a9047ab24 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -84,6 +84,56 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T13:42:37.634355"
+        "timestamp": "2025-12-18T15:30:09.343629"
+    },
+    "rgi/bwt - homo_sapiens - test_fastq_gz": {
+        "content": [
+            [
+                "versions.yml:md5,b58eb6cbad22c5eb956ad02a190a4e42"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.allele_mapping_data.txt:md5,b4026da308ca791aad88f0ed0792e752",
+                        "test.artifacts_mapping_stats.txt:md5,dc3ec8afe253950acb86b3ecd9dabba4",
+                        "test.coverage.temp.txt:md5,660631842fc316d1b1081c3d8109c817",
+                        "test.coverage_all_positions.summary.temp.txt:md5,05c4ab1a8e600535beef1c4745fa6fba",
+                        "test.coverage_all_positions.temp.txt:md5,7d8071acc4745847d612d2ceb0964291",
+                        "test.gene_mapping_data.txt:md5,fc75b9923a2a4e4ff534f9d1d7dfae56",
+                        "test.overall_mapping_stats.txt:md5,16b52dbfd9d3f8e0d5c87e153a0b5276",
+                        "test.reference_mapping_stats.txt:md5,8c7c19c11274ec1bf7ee51f4b1e8a0be",
+                        "test.seqs.temp.txt:md5,94a9ffa4649f9919454cf2e3606f35e2",
+                        "test.temp.txt:md5,6f1d013552a1b03a490bb33c909c5e74"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.allele_mapping_data.json:md5,13fef6bc037c98b6a8642f2ad7ee345f"
+                ]
+            ],
+            [
+                "test.temp.sam.temp.fsa"
+            ],
+            [
+                "6.0.5"
+            ],
+            [
+                "4.0.1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-18T15:29:41.02051"
     }
 }
\ No newline at end of file

From 47300b443bc50d73a595e165f7917a0057701390 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 15:43:48 +1100
Subject: [PATCH 07/18] rgi/bwt: update snapshot

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

diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
index 351a9047ab24..867886f9dd4e 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -106,7 +106,7 @@
                         "test.gene_mapping_data.txt:md5,fc75b9923a2a4e4ff534f9d1d7dfae56",
                         "test.overall_mapping_stats.txt:md5,16b52dbfd9d3f8e0d5c87e153a0b5276",
                         "test.reference_mapping_stats.txt:md5,8c7c19c11274ec1bf7ee51f4b1e8a0be",
-                        "test.seqs.temp.txt:md5,94a9ffa4649f9919454cf2e3606f35e2",
+                        "test.seqs.temp.txt:md5,819f4fe54d72e635f388b1cfa0ac9058",
                         "test.temp.txt:md5,6f1d013552a1b03a490bb33c909c5e74"
                     ]
                 ]

From c95108caef85343a23ec15581ede8dca29301824 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 15:50:59 +1100
Subject: [PATCH 08/18] rgi/bwt: fix tests

  - Don't check temp/ directory on snapshot, is different every time
  - Update snapshot
---
 modules/nf-core/rgi/bwt/tests/main.nf.test      | 1 -
 modules/nf-core/rgi/bwt/tests/main.nf.test.snap | 9 +++------
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test b/modules/nf-core/rgi/bwt/tests/main.nf.test
index 075df33db1bb..d189e8de1154 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test
@@ -60,7 +60,6 @@ nextflow_process {
                     process.out.versions,
                     process.out.tsv,
                     process.out.json,
-                    file(process.out.tmp.get(0).get(1)).list().sort(),
                     process.out.tool_version,
                     process.out.db_version,
                     ).match() }
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
index 867886f9dd4e..753f6d8582fe 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -84,7 +84,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T15:30:09.343629"
+        "timestamp": "2025-12-18T15:50:19.844883"
     },
     "rgi/bwt - homo_sapiens - test_fastq_gz": {
         "content": [
@@ -106,7 +106,7 @@
                         "test.gene_mapping_data.txt:md5,fc75b9923a2a4e4ff534f9d1d7dfae56",
                         "test.overall_mapping_stats.txt:md5,16b52dbfd9d3f8e0d5c87e153a0b5276",
                         "test.reference_mapping_stats.txt:md5,8c7c19c11274ec1bf7ee51f4b1e8a0be",
-                        "test.seqs.temp.txt:md5,819f4fe54d72e635f388b1cfa0ac9058",
+                        "test.seqs.temp.txt:md5,b70ab46abd10edbca8710abffe457553",
                         "test.temp.txt:md5,6f1d013552a1b03a490bb33c909c5e74"
                     ]
                 ]
@@ -120,9 +120,6 @@
                     "test.allele_mapping_data.json:md5,13fef6bc037c98b6a8642f2ad7ee345f"
                 ]
             ],
-            [
-                "test.temp.sam.temp.fsa"
-            ],
             [
                 "6.0.5"
             ],
@@ -134,6 +131,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T15:29:41.02051"
+        "timestamp": "2025-12-18T15:49:45.276248"
     }
 }
\ No newline at end of file

From e90b13c4294e652a97168c66c42552d63789eec5 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 16:27:29 +1100
Subject: [PATCH 09/18] rgi/bwt: continue to fix tests

  - provide input.reads as list
  - don't check tsv snapshot (it's different every time)
---
 modules/nf-core/rgi/bwt/tests/main.nf.test | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test b/modules/nf-core/rgi/bwt/tests/main.nf.test
index d189e8de1154..2db4226175a1 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test
@@ -36,7 +36,6 @@ nextflow_process {
         }
     }
 
-
     test("rgi/bwt - homo_sapiens - test_fastq_gz") {
 
         when {
@@ -44,8 +43,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+                    [
+                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+                    ]
                 ]
                 input[1] = RGI_CARDANNOTATION.out.db
                 input[2] = []
@@ -58,8 +59,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.versions,
-                    process.out.tsv,
                     process.out.json,
+                    file(process.out.tmp.get(0).get(1)).list().sort(),
                     process.out.tool_version,
                     process.out.db_version,
                     ).match() }
@@ -76,8 +77,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+                    [
+                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true),
+                    ]
                 ]
                 input[1] = RGI_CARDANNOTATION.out.db
                 input[2] = []

From 8db057402a5d8a99597788a8fe7b0d76ed69bce8 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 18 Dec 2025 16:48:16 +1100
Subject: [PATCH 10/18] rgi/bwt: remove json from snapshots

  - json files are in random order so snapshot differs every time (I think)
---
 modules/nf-core/rgi/bwt/tests/main.nf.test    |  1 -
 .../nf-core/rgi/bwt/tests/main.nf.test.snap   | 32 ++-----------------
 2 files changed, 3 insertions(+), 30 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test b/modules/nf-core/rgi/bwt/tests/main.nf.test
index 2db4226175a1..dc33b4c5d178 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test
@@ -59,7 +59,6 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.versions,
-                    process.out.json,
                     file(process.out.tmp.get(0).get(1)).list().sort(),
                     process.out.tool_version,
                     process.out.db_version,
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
index 753f6d8582fe..45280276f858 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -84,7 +84,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T15:50:19.844883"
+        "timestamp": "2025-12-18T16:46:01.907563"
     },
     "rgi/bwt - homo_sapiens - test_fastq_gz": {
         "content": [
@@ -92,33 +92,7 @@
                 "versions.yml:md5,b58eb6cbad22c5eb956ad02a190a4e42"
             ],
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    [
-                        "test.allele_mapping_data.txt:md5,b4026da308ca791aad88f0ed0792e752",
-                        "test.artifacts_mapping_stats.txt:md5,dc3ec8afe253950acb86b3ecd9dabba4",
-                        "test.coverage.temp.txt:md5,660631842fc316d1b1081c3d8109c817",
-                        "test.coverage_all_positions.summary.temp.txt:md5,05c4ab1a8e600535beef1c4745fa6fba",
-                        "test.coverage_all_positions.temp.txt:md5,7d8071acc4745847d612d2ceb0964291",
-                        "test.gene_mapping_data.txt:md5,fc75b9923a2a4e4ff534f9d1d7dfae56",
-                        "test.overall_mapping_stats.txt:md5,16b52dbfd9d3f8e0d5c87e153a0b5276",
-                        "test.reference_mapping_stats.txt:md5,8c7c19c11274ec1bf7ee51f4b1e8a0be",
-                        "test.seqs.temp.txt:md5,b70ab46abd10edbca8710abffe457553",
-                        "test.temp.txt:md5,6f1d013552a1b03a490bb33c909c5e74"
-                    ]
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.allele_mapping_data.json:md5,13fef6bc037c98b6a8642f2ad7ee345f"
-                ]
+                "test.temp.sam.temp.fsa"
             ],
             [
                 "6.0.5"
@@ -131,6 +105,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T15:49:45.276248"
+        "timestamp": "2025-12-18T16:45:23.269447"
     }
 }
\ No newline at end of file

From cd2faf4ef2d1a60efd064ae53c96f7f4f3227579 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 30 Dec 2025 14:35:46 +1000
Subject: [PATCH 11/18] rgi/bwt: remove task.ext value

  - Use '--local' flag as default
---
 modules/nf-core/rgi/bwt/main.nf | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index f77ed7700ae6..028c9f5ee1e4 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -25,13 +25,6 @@ process RGI_BWT {
 
     script:
     def args = task.ext.args ?: ''
-    def use_local = task.ext.local == null ? true : task.ext.local as boolean
-    // Add this to nextflow.config if not using local:
-    // withName: RGI_BWT {
-    //      ext.local = false
-    //  }
-    def local_flag = use_local ? '--local' : ''
-    // This customizes the command: rgi bwt
     def prefix = task.ext.prefix ?: "${meta.id}"
     def read_one = reads instanceof List ? reads[0] : reads
     def read_two = reads instanceof List && reads.size() > 1 ? reads[1] : null
@@ -54,7 +47,7 @@ process RGI_BWT {
     rgi \\
         load \\
         ${args} \\
-        ${local_flag} \\
+        --local \\
         --card_json ${card}/card.json \\
         --debug \\
         --card_annotation ${card}/card_database_v\$DB_VERSION.fasta \\
@@ -64,7 +57,7 @@ process RGI_BWT {
     rgi \\
         bwt \\
         ${args} \\
-        ${local_flag} \\
+        --local \\
         --threads ${task.cpus} \\
         --output_file ${prefix} \\
         --read_one ${read_one} \\

From c1673365bfdc4bcb8ef88ed0ec4a0d438b6ce1a4 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 15 Jan 2026 12:29:22 +1100
Subject: [PATCH 12/18] rgi/bwt: move version to topics output

  - Code review from #9585
---
 modules/nf-core/rgi/bwt/main.nf               | 19 +------
 .../nf-core/rgi/bwt/tests/main.nf.test.snap   | 52 ++++++++++---------
 2 files changed, 30 insertions(+), 41 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 028c9f5ee1e4..890a2d7bb664 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -16,9 +16,8 @@ process RGI_BWT {
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt"), emit: tsv
     tuple val(meta), path("temp/"), emit: tmp
-    env RGI_VERSION, emit: tool_version
-    env DB_VERSION, emit: db_version
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('rgi')         , eval('rgi main --version') , emit: versions_rgi, topic: versions
+    tuple val("${task.process}"), val('rgi-database'), eval('echo $DB_VERSION')   , emit: versions_db , topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -67,13 +66,6 @@ process RGI_BWT {
     mkdir temp/
     for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e \$FILE ]] && mv \$FILE temp/; done
 
-    RGI_VERSION=\$(rgi main --version)
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rgi: \$(echo \$RGI_VERSION)
-        rgi-database: \$(echo \$DB_VERSION)
-    END_VERSIONS
     """
 
     stub:
@@ -82,13 +74,6 @@ process RGI_BWT {
     touch test.json
     touch test.txt
 
-    RGI_VERSION=\$(rgi main --version)
     DB_VERSION=stub_version
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rgi: \$(echo \$RGI_VERSION)
-        rgi-database: \$(echo \$DB_VERSION)
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
index 45280276f858..7a792cd8b5f9 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -32,16 +32,18 @@
                     ]
                 ],
                 "3": [
-                    "6.0.5"
+                    [
+                        "RGI_BWT",
+                        "rgi",
+                        "6.0.5"
+                    ]
                 ],
                 "4": [
-                    "stub_version"
-                ],
-                "5": [
-                    "versions.yml:md5,47cb67c7969fe73d5f59c5fee0cda9c6"
-                ],
-                "db_version": [
-                    "stub_version"
+                    [
+                        "RGI_BWT",
+                        "rgi-database",
+                        "stub_version"
+                    ]
                 ],
                 "json": [
                     [
@@ -63,9 +65,6 @@
                         ]
                     ]
                 ],
-                "tool_version": [
-                    "6.0.5"
-                ],
                 "tsv": [
                     [
                         {
@@ -75,8 +74,19 @@
                         "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,47cb67c7969fe73d5f59c5fee0cda9c6"
+                "versions_db": [
+                    [
+                        "RGI_BWT",
+                        "rgi-database",
+                        "stub_version"
+                    ]
+                ],
+                "versions_rgi": [
+                    [
+                        "RGI_BWT",
+                        "rgi",
+                        "6.0.5"
+                    ]
                 ]
             }
         ],
@@ -84,27 +94,21 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T16:46:01.907563"
+        "timestamp": "2026-01-15T12:26:59.982426"
     },
     "rgi/bwt - homo_sapiens - test_fastq_gz": {
         "content": [
-            [
-                "versions.yml:md5,b58eb6cbad22c5eb956ad02a190a4e42"
-            ],
+            null,
             [
                 "test.temp.sam.temp.fsa"
             ],
-            [
-                "6.0.5"
-            ],
-            [
-                "4.0.1"
-            ]
+            null,
+            null
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-12-18T16:45:23.269447"
+        "timestamp": "2026-01-15T12:26:25.450504"
     }
 }
\ No newline at end of file

From 6efbbe375d95c6073e4fc004e7392a79a6457332 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Thu, 15 Jan 2026 12:29:47 +1100
Subject: [PATCH 13/18] rgi/bwt: update meta.yml

  - Create topics field in meta.yml
---
 modules/nf-core/rgi/bwt/meta.yml | 51 +++++++++++++++++++++-----------
 1 file changed, 34 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
index 43210e91d392..7fdb3394d795 100644
--- a/modules/nf-core/rgi/bwt/meta.yml
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -29,7 +29,8 @@ input:
         type: file
         description: Nucleotide sequences in FASTQ or FASTA format
         pattern: "*.{fastq,fastq.gz,fq,fq.gz,fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_1930 # FASTQ
   - card:
       type: directory
       description: Directory containing the CARD database. This is expected to be
@@ -76,23 +77,39 @@ output:
           type: directory
           description: Directory containing various intermediate files
           pattern: "temp/"
-  tool_version:
-    - RGI_VERSION:
-        type: string
-        description: The version of the tool in string format (useful for
-          downstream tools such as hAMRronization)
-  db_version:
-    - DB_VERSION:
-        type: string
-        description: The version of the used database in string format (useful for
-          downstream tools such as hAMRronization)
+  versions_rgi:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rgi:
+          type: string
+          description: The tool name
+      - rgi main --version:
+          type: string
+          description: The version string returned by the command
+  versions_db:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rgi-database:
+          type: string
+          description: The tool name
+      - echo $DB_VERSION:
+          type: string
+          description: The CARD database version string
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rgi:
+          type: string
+          description: The tool name
+      - rgi main --version:
+          type: string
+          description: The command used to generate the version of the tool
+
 authors:
   - "@vinisalazar"
 maintainers:

From b1f3cae5077174f00deb1c7a979df6e019039aff Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Mon, 19 Jan 2026 10:34:21 +1100
Subject: [PATCH 14/18] Apply suggestions from code review

Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/nf-core/rgi/bwt/main.nf  | 9 ++++++---
 modules/nf-core/rgi/bwt/meta.yml | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 890a2d7bb664..ee99b299c071 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -8,7 +8,7 @@ process RGI_BWT {
         : 'biocontainers/rgi:6.0.5--pyh05cac1d_0'}"
 
     input:
-    tuple val(meta), path(reads)
+    tuple val(meta), path(reads, arity: '1..2')
     path card
     path wildcard
 
@@ -23,10 +23,13 @@ process RGI_BWT {
     task.ext.when == null || task.ext.when
 
     script:
+    // This customizes the command: rgi load
     def args = task.ext.args ?: ''
+    // This customizes the command: rgi main
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def read_one = reads instanceof List ? reads[0] : reads
-    def read_two = reads instanceof List && reads.size() > 1 ? reads[1] : null
+    def read_one = reads[0]
+    def read_two = reads.size() > 1 ? reads[1] : null
     def load_wildcard = ""
 
     if (wildcard) {
diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
index 7fdb3394d795..7838e8d69dc7 100644
--- a/modules/nf-core/rgi/bwt/meta.yml
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -27,7 +27,7 @@ input:
           e.g. [ id:'test', single_end:false ]
     - reads:
         type: file
-        description: Nucleotide sequences in FASTQ or FASTA format
+        description: Single-end or paired-end nucleotide sequences in FASTQ or FASTA format
         pattern: "*.{fastq,fastq.gz,fq,fq.gz,fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
         ontologies:
           - edam: http://edamontology.org/format_1930 # FASTQ

From 890342982c70d35552ce508fbe923e7688b43e46 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 20 Jan 2026 14:07:50 +1100
Subject: [PATCH 15/18] rgi/bwt: fix tests and linting

  - capture topics appropriately in meta.yml
---
 modules/nf-core/rgi/bwt/main.nf               |  4 +--
 modules/nf-core/rgi/bwt/meta.yml              | 13 ++++++++--
 modules/nf-core/rgi/bwt/tests/main.nf.test    |  4 +--
 .../nf-core/rgi/bwt/tests/main.nf.test.snap   | 25 ++++++++++++++-----
 4 files changed, 33 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index ee99b299c071..4fc467e73b64 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -16,8 +16,8 @@ process RGI_BWT {
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt"), emit: tsv
     tuple val(meta), path("temp/"), emit: tmp
-    tuple val("${task.process}"), val('rgi')         , eval('rgi main --version') , emit: versions_rgi, topic: versions
-    tuple val("${task.process}"), val('rgi-database'), eval('echo $DB_VERSION')   , emit: versions_db , topic: versions
+    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version") , emit: versions_rgi, topic: versions
+    tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION")   , emit: versions_db , topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
index 7838e8d69dc7..c6b2a639711b 100644
--- a/modules/nf-core/rgi/bwt/meta.yml
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -94,7 +94,7 @@ output:
       - rgi-database:
           type: string
           description: The tool name
-      - echo $DB_VERSION:
+      - echo \$DB_VERSION:
           type: string
           description: The CARD database version string
 
@@ -108,7 +108,16 @@ topics:
           description: The tool name
       - rgi main --version:
           type: string
-          description: The command used to generate the version of the tool
+          description: Command used to collect the version
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rgi-database:
+          type: string
+          description: The tool name
+      - echo $DB_VERSION:
+          type: string
+          description: Command used to collect the version
 
 authors:
   - "@vinisalazar"
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test b/modules/nf-core/rgi/bwt/tests/main.nf.test
index dc33b4c5d178..40074303c71a 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test
@@ -58,10 +58,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
                     file(process.out.tmp.get(0).get(1)).list().sort(),
-                    process.out.tool_version,
-                    process.out.db_version,
                     ).match() }
             )
         }
diff --git a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
index 7a792cd8b5f9..91124f320ec6 100644
--- a/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
+++ b/modules/nf-core/rgi/bwt/tests/main.nf.test.snap
@@ -94,21 +94,34 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2026-01-15T12:26:59.982426"
+        "timestamp": "2026-01-20T14:01:51.787935"
     },
     "rgi/bwt - homo_sapiens - test_fastq_gz": {
         "content": [
-            null,
+            {
+                "versions_db": [
+                    [
+                        "RGI_BWT",
+                        "rgi-database",
+                        "4.0.1"
+                    ]
+                ],
+                "versions_rgi": [
+                    [
+                        "RGI_BWT",
+                        "rgi",
+                        "6.0.5"
+                    ]
+                ]
+            },
             [
                 "test.temp.sam.temp.fsa"
-            ],
-            null,
-            null
+            ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2026-01-15T12:26:25.450504"
+        "timestamp": "2026-01-20T14:01:20.471757"
     }
 }
\ No newline at end of file

From a63bb29e894e7c7322f44c78fae88628e40062a8 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 20 Jan 2026 14:23:01 +1100
Subject: [PATCH 16/18] rgi/bwt: formatting

---
 modules/nf-core/rgi/bwt/main.nf  | 2 +-
 modules/nf-core/rgi/bwt/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 4fc467e73b64..154af42a01e0 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -16,7 +16,7 @@ process RGI_BWT {
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt"), emit: tsv
     tuple val(meta), path("temp/"), emit: tmp
-    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version") , emit: versions_rgi, topic: versions
+    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version")  , emit: versions_rgi, topic: versions
     tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION")   , emit: versions_db , topic: versions
 
     when:
diff --git a/modules/nf-core/rgi/bwt/meta.yml b/modules/nf-core/rgi/bwt/meta.yml
index c6b2a639711b..a29a5c3f838f 100644
--- a/modules/nf-core/rgi/bwt/meta.yml
+++ b/modules/nf-core/rgi/bwt/meta.yml
@@ -115,7 +115,7 @@ topics:
       - rgi-database:
           type: string
           description: The tool name
-      - echo $DB_VERSION:
+      - echo \$DB_VERSION:
           type: string
           description: Command used to collect the version
 

From 6647bb8e32057785a0909786cadeae854e0ee6cc Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 20 Jan 2026 14:31:02 +1100
Subject: [PATCH 17/18] rgi/bwt: formatting

---
 modules/nf-core/rgi/bwt/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 154af42a01e0..7f0c8492aaf8 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -16,8 +16,8 @@ process RGI_BWT {
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt"), emit: tsv
     tuple val(meta), path("temp/"), emit: tmp
-    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version")  , emit: versions_rgi, topic: versions
-    tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION")   , emit: versions_db , topic: versions
+    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version"), emit: versions_rgi, topic: versions
+    tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION"),  emit: versions_db , topic: versions
 
     when:
     task.ext.when == null || task.ext.when

From 60c83c31e9d598471db35c3c853395c860028043 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 20 Jan 2026 14:35:03 +1100
Subject: [PATCH 18/18] rgi/bwt: formatting

---
 modules/nf-core/rgi/bwt/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/rgi/bwt/main.nf b/modules/nf-core/rgi/bwt/main.nf
index 7f0c8492aaf8..a69f3a089736 100644
--- a/modules/nf-core/rgi/bwt/main.nf
+++ b/modules/nf-core/rgi/bwt/main.nf
@@ -16,8 +16,8 @@ process RGI_BWT {
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt"), emit: tsv
     tuple val(meta), path("temp/"), emit: tmp
-    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version"), emit: versions_rgi, topic: versions
-    tuple val("${task.process}"), val('rgi-database'), eval("echo \$DB_VERSION"),  emit: versions_db , topic: versions
+    tuple val("${task.process}"), val('rgi')         , eval("rgi main --version"),  emit: versions_rgi, topic: versions
+    tuple val("${task.process}"), val('rgi-database'), eval("echo \\$DB_VERSION"),  emit: versions_db , topic: versions
 
     when:
     task.ext.when == null || task.ext.when