Repository: nf-core/modules
Pull request #7726: `ARTIC_MINION` migration to nf-test
Author: login: LouisLeNezet
Labels: name: nf-test
Created: 2025-03-02T11:39:14Z | Merged: 2025-03-03T09:30:57Z

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## PR checklist

Closes #7532

- [ ] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] If you've added a new tool - have you followed the module conventions in the [contribution docs](https://github.com/nf-core/modules/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, include test data in your PR.
- [ ] Remove all TODO statements.
- [ ] Emit the `versions.yml` file.
- [ ] Follow the naming conventions.
- [ ] Follow the parameters requirements.
- [ ] Follow the input/output options guidelines.
- [ ] Add a resource `label`
- [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
- Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  - For modules:
    - [ ] `nf-core modules test <MODULE> --profile docker`
    - [ ] `nf-core modules test <MODULE> --profile singularity`
    - [ ] `nf-core modules test <MODULE> --profile conda`
  - For subworkflows:
    - [ ] `nf-core subworkflows test <SUBWORKFLOW> --profile docker`
    - [ ] `nf-core subworkflows test <SUBWORKFLOW> --profile singularity`
    - [ ] `nf-core subworkflows test <SUBWORKFLOW> --profile conda`


Linked issue #7532: nf-test migration: artic/minion

Diff:
diff --git a/modules/nf-core/artic/minion/environment.yml b/modules/nf-core/artic/minion/environment.yml
index fd739b2cf0d6..a0a6221d7722 100644
--- a/modules/nf-core/artic/minion/environment.yml
+++ b/modules/nf-core/artic/minion/environment.yml
@@ -4,4 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::artic=1.2.3
+  - bioconda::artic=1.6.1
+  - bioconda::htslib=1.17
diff --git a/modules/nf-core/artic/minion/main.nf b/modules/nf-core/artic/minion/main.nf
index 8559bd75c8b8..2f9a7c9ccf6b 100644
--- a/modules/nf-core/artic/minion/main.nf
+++ b/modules/nf-core/artic/minion/main.nf
@@ -4,19 +4,13 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
-    path  sequencing_summary
-    path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
-    path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
-    path  medaka_model_file
-    val   medaka_model_string
-    val   scheme
-    val   scheme_version
+    tuple val(meta2), path(model_dir), val(model)
+    tuple val(meta3), path(fasta), path(bed)
 
     output:
     tuple val(meta), path("${prefix}.*")                              , emit: results
@@ -38,17 +32,8 @@ process ARTIC_MINION {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
-    def version  = scheme_version.toString().toLowerCase().replaceAll('v','')
-    def fast5    = fast5_dir ? "--fast5-directory $fast5_dir"             : ""
-    def summary  = sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
-    def model    = ""
-    if (args.tokenize().contains('--medaka')) {
-        fast5   = ""
-        summary = ""
-        model   = medaka_model_file ? "--medaka-model ./$medaka_model_file" : "--medaka-model $medaka_model_string"
-    }
+    def model_dir_cmd   = model_dir   ? "--model-dir $model_dir" : "--model-dir \$(which artic | sed 's/artic/models/')"
     def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
-    def VERSION = '1.2.3' // WARN: Version information provided by tool on CLI is incorrect. Please update this string when bumping container versions.
     """
     $hd5_plugin_path
 
@@ -57,17 +42,67 @@ process ARTIC_MINION {
         $args \\
         --threads $task.cpus \\
         --read-file $fastq \\
-        --scheme-directory ./primer-schemes \\
-        --scheme-version $version \\
-        $model \\
-        $fast5 \\
-        $summary \\
-        $scheme \\
+        --bed $bed \\
+        --ref $fasta \\
+        $model_dir_cmd \\
+        --model $model \\
         $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        artic: $VERSION
+        artic: \$(artic -v 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.1.trimmed.rg.sorted.bam
+    touch ${prefix}.1.trimmed.rg.sorted.bai
+    touch ${prefix}.1.vcf
+    touch ${prefix}.2.trimmed.rg.sorted.bam
+    touch ${prefix}.2.trimmed.rg.sorted.bai
+    touch ${prefix}.2.vcf
+
+    touch ${prefix}.alignreport.csv
+    touch ${prefix}.amplicon_depths.tsv
+
+    touch ${prefix}.consensus.fasta
+    touch ${prefix}.coverage_mask.txt
+    touch ${prefix}.coverage_mask.txt.1.depths
+    touch ${prefix}.coverage_mask.txt.2.depths
+
+    touch ${prefix}.fail.vcf
+
+    touch ${prefix}.merged.vcf
+    echo "" | gzip > ${prefix}.merged.vcf.gz
+    touch ${prefix}.merged.vcf.tbi
+
+    touch ${prefix}.minion.log.txt
+
+    echo "" | gzip > ${prefix}.normalised.vcf.gz
+    touch ${prefix}.normalised.vcf.tbi
+
+    touch ${prefix}.pass.vcf
+    echo "" | gzip > ${prefix}.pass.vcf.gz
+    touch ${prefix}.pass.vcf.gz.tbi
+
+    touch ${prefix}.preconsensus.fasta
+    touch ${prefix}.preconsensus.fasta.fai
+
+    touch ${prefix}.primers.vcf
+    touch ${prefix}.primersitereport.txt
+    touch ${prefix}.primertrimmed.rg.sorted.bam
+    touch ${prefix}.primertrimmed.rg.sorted.bam.bai
+
+    touch ${prefix}.sorted.bam
+    touch ${prefix}.sorted.bam.bai
+    touch ${prefix}.trimmed.rg.sorted.bam
+    touch ${prefix}.trimmed.rg.sorted.bam.bai
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        artic: \$(artic -v 2>&1 | sed 's/^.*artic //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/artic/minion/meta.yml b/modules/nf-core/artic/minion/meta.yml
index 3c90d62272d0..bf942310f748 100644
--- a/modules/nf-core/artic/minion/meta.yml
+++ b/modules/nf-core/artic/minion/meta.yml
@@ -24,36 +24,33 @@ input:
         type: file
         description: FastQ file containing reads
         pattern: "*.{fastq.gz}"
-  - - fast5_dir:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing model information
+          e.g. [ id:'test', single_end:false ]
+    - model_dir:
         type: directory
-        description: Directory containing MinION FAST5 files
+        description: Path containing clair3 models, defaults to models packaged with conda installation
         pattern: "*"
-  - - sequencing_summary:
-        type: file
-        description: Path to Guppy sequencing summary
-        pattern: "*.{txt}"
-  - - '"primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta"':
+    - model:
+        type: string
+        description: |
+          The model to use for clair3, if not provided the pipeline will try to figure
+          it out the appropriate model from the read fastq
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing scheme information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
         type: file
-        description: Scheme reference file
-  - - '"primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed"':
+        description: Scheme reference fasta file
+        pattern: "*.{fasta}"
+    - bed:
         type: file
         description: Scheme BED file
-  - - medaka_model_file:
-        type: file
-        description: |
-          Medaka model file to use (if option --medaka is set)
-        pattern: "*.hdf5"
-  - - medaka_model_string:
-        type: string
-        description: |
-          Medaka model string to use (if option --medaka is set)
-        pattern: "*"
-  - - scheme:
-        type: string
-        description: Name of the primer scheme
-  - - scheme_version:
-        type: string
-        description: Version of the primer scheme
+        pattern: "*.{bed}"
 output:
   - results:
       - meta:
diff --git a/modules/nf-core/artic/minion/tests/main.nf.test b/modules/nf-core/artic/minion/tests/main.nf.test
new file mode 100644
index 000000000000..433205cde8ef
--- /dev/null
+++ b/modules/nf-core/artic/minion/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process ARTIC_MINION"
+
+    script "../main.nf"
+    process "ARTIC_MINION"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+    tag "artic"
+    tag "artic/minion"
+
+    test("sarscov2 - fastq") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists:true)
+                ]
+                input[1] = [[id: 'model'], [], "hifi"]
+                input[2] = [
+                    [id: "nCov-2019", version: "3.0.0"],
+                    file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists:true),
+                    file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists:true)
+                ]
+                """
+            }
+        }
+        then {
+            def fileNames = process.out.results.collect { result ->
+                def files = result[1]
+                files.collect { filePath ->
+                    def f = file(filePath)
+                    f.directory ? f.listFiles().name : f.name
+                }
+            }
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    fileNames,
+                    process.out.bam.collect{ file(it[1]).name },
+                    process.out.bai,
+                    process.out.bam_trimmed.collect{ file(it[1]).name },
+                    process.out.bai_trimmed,
+                    process.out.bam_primertrimmed.collect{ file(it[1]).name },
+                    process.out.bai_primertrimmed,
+                    process.out.fasta,
+                    process.out.vcf.collect{ file(it[1]).name },
+                    process.out.tbi,
+                    process.out.json
+                ).match() }
+            )
+        }
+    }
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists:true)
+                ]
+                input[1] = [[id: 'model'], [], "hifi"]
+                input[2] = [
+                    [id: "nCov-2019", version: "3.0.0"],
+                    file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists:true),
+                    file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists:true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/artic/minion/tests/main.nf.test.snap b/modules/nf-core/artic/minion/tests/main.nf.test.snap
new file mode 100644
index 000000000000..eae31144b6d4
--- /dev/null
+++ b/modules/nf-core/artic/minion/tests/main.nf.test.snap
@@ -0,0 +1,379 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.1.trimmed.rg.sorted.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.1.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.trimmed.rg.sorted.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.alignreport.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.amplicon_depths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.consensus.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.coverage_mask.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.coverage_mask.txt.1.depths:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.coverage_mask.txt.2.depths:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.fail.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.merged.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.merged.vcf.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.minion.log.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.normalised.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.normalised.vcf.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pass.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pass.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.pass.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.preconsensus.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.preconsensus.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primers.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primersitereport.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primertrimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primertrimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.trimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    
+                ],
+                "11": [
+                    "versions.yml:md5,f76ecd36f1daeb56daeb64400adf160b"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.trimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.primertrimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.primertrimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.consensus.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pass.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pass.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bai_primertrimmed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.primertrimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bai_trimmed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.trimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_primertrimmed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.primertrimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam_trimmed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.consensus.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test.1.trimmed.rg.sorted.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.1.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.trimmed.rg.sorted.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.alignreport.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.amplicon_depths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.consensus.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.coverage_mask.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.coverage_mask.txt.1.depths:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.coverage_mask.txt.2.depths:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.fail.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.merged.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.merged.vcf.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.minion.log.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.normalised.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.normalised.vcf.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pass.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.pass.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test.pass.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.preconsensus.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.preconsensus.fasta.fai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primers.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primersitereport.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primertrimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.primertrimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.trimmed.rg.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test.trimmed.rg.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pass.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.pass.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f76ecd36f1daeb56daeb64400adf160b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-02T13:22:56.372935027"
+    },
+    "sarscov2 - fastq": {
+        "content": [
+            [
+                "versions.yml:md5,f76ecd36f1daeb56daeb64400adf160b"
+            ],
+            [
+                [
+                    "test.1.trimmed.rg.sorted.bam",
+                    "test.1.trimmed.rg.sorted.bam.bai",
+                    "test.1.vcf",
+                    "test.2.trimmed.rg.sorted.bam",
+                    "test.2.trimmed.rg.sorted.bam.bai",
+                    "test.2.vcf",
+                    "test.alignreport.csv",
+                    "test.amplicon_depths.tsv",
+                    "test.consensus.fasta",
+                    "test.coverage_mask.txt",
+                    "test.coverage_mask.txt.1.depths",
+                    "test.coverage_mask.txt.2.depths",
+                    "test.fail.vcf",
+                    "test.merged.vcf",
+                    "test.merged.vcf.gz",
+                    "test.merged.vcf.gz.tbi",
+                    "test.minion.log.txt",
+                    "test.normalised.vcf.gz",
+                    "test.normalised.vcf.gz.tbi",
+                    "test.pass.vcf",
+                    "test.pass.vcf.gz",
+                    "test.pass.vcf.gz.tbi",
+                    "test.preconsensus.fasta",
+                    "test.preconsensus.fasta.fai",
+                    "test.primers.vcf",
+                    "test.primersitereport.txt",
+                    "test.primertrimmed.rg.sorted.bam",
+                    "test.primertrimmed.rg.sorted.bam.bai",
+                    "test.sorted.bam",
+                    "test.sorted.bam.bai",
+                    "test.trimmed.rg.sorted.bam",
+                    "test.trimmed.rg.sorted.bam.bai"
+                ]
+            ],
+            [
+                "test.sorted.bam"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.sorted.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ]
+            ],
+            [
+                "test.trimmed.rg.sorted.bam"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.trimmed.rg.sorted.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ]
+            ],
+            [
+                "test.primertrimmed.rg.sorted.bam"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.primertrimmed.rg.sorted.bam.bai:md5,0d76977b2e36046cc176112776c5fa4e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.consensus.fasta:md5,ab9bbc82f542c9eed46808c640aa7a1e"
+                ]
+            ],
+            [
+                "test.pass.vcf.gz"
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.pass.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                ]
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-02T13:25:08.780155357"
+    }
+}
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 995dd615660a..9cc198992cdb 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1,6 +1,3 @@
-artic/minion:
-  - modules/nf-core/artic/minion/**
-  - tests/modules/nf-core/artic/minion/**
 ascat:
   - modules/nf-core/ascat/**
   - tests/modules/nf-core/ascat/**
diff --git a/tests/modules/nf-core/artic/minion/main.nf b/tests/modules/nf-core/artic/minion/main.nf
deleted file mode 100644
index 4a47f5636553..000000000000
--- a/tests/modules/nf-core/artic/minion/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR        } from '../../../../../modules/nf-core/untar/main.nf'
-include { ARTIC_MINION } from '../../../../../modules/nf-core/artic/minion/main.nf'
-
-workflow test_artic_minion {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
-    ]
-    fast5_tar          = [ [], file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
-    sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
-    fasta              = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
-    bed                = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
-
-    fast5_dir = UNTAR ( fast5_tar ).untar.map{ it[1] }
-
-    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
-}
diff --git a/tests/modules/nf-core/artic/minion/nextflow.config b/tests/modules/nf-core/artic/minion/nextflow.config
deleted file mode 100644
index 8730f1c4b930..000000000000
--- a/tests/modules/nf-core/artic/minion/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/artic/minion/test.yml b/tests/modules/nf-core/artic/minion/test.yml
deleted file mode 100644
index 5f444dc9e97e..000000000000
--- a/tests/modules/nf-core/artic/minion/test.yml
+++ /dev/null
@@ -1,260 +0,0 @@
-- name: artic minion
-  command: nextflow run ./tests/modules/nf-core/artic/minion -entry test_artic_minion -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/artic/minion/nextflow.config
-  tags:
-    - artic
-    - artic/minion
-  files:
-    - path: output/artic/test.1.vcf
-      md5sum: f0278719cbb853addcad74b73d810a24
-    - path: output/artic/test.2.vcf
-      md5sum: f0278719cbb853addcad74b73d810a24
-    - path: output/artic/test.alignreport.er
-      md5sum: ddfff35c7ebc9837530c78f7a213cea0
-    - path: output/artic/test.alignreport.txt
-      md5sum: 0fcadf1467ac253476b2d43bbfa36616
-    - path: output/artic/test.consensus.fasta
-      md5sum: 96e49e6995ca459606a2c00cfc2d6263
-    - path: output/artic/test.coverage_mask.txt
-      md5sum: 7abd414756c444c86766123a60687ed1
-    - path: output/artic/test.coverage_mask.txt.1.depths
-      md5sum: d4170a48491e12f34b0a15a336bdf5e6
-    - path: output/artic/test.coverage_mask.txt.2.depths
-      md5sum: 130f85d80c22fccc3e0bbd9de12d310d
-    - path: output/artic/test.fail.vcf
-      md5sum: e6e184f1fa153868e3acea0eab42e484
-    - path: output/artic/test.fastq.gz.index
-      md5sum: c42d917f12840ebc9bd21ee112c88aa0
-    - path: output/artic/test.fastq.gz.index.fai
-      md5sum: 81d718eeaaaae68cb33003f56194e956
-    - path: output/artic/test.fastq.gz.index.gzi
-      md5sum: 7dea362b3fac8e00956a4952a3d4f474
-    - path: output/artic/test.fastq.gz.index.readdb
-      md5sum: 3c6296842e91578db93688b4021c8947
-    - path: output/artic/test.merged.vcf
-      md5sum: e6e184f1fa153868e3acea0eab42e484
-    - path: output/artic/test.minion.log.txt
-      contains:
-        - "artic_vcf_merge"
-    - path: output/artic/test.muscle.in.fasta
-      md5sum: 6152dfcbf4b6b4d2101bbd0aaed89eba
-    - path: output/artic/test.muscle.out.fasta
-      md5sum: 6152dfcbf4b6b4d2101bbd0aaed89eba
-    - path: output/artic/test.pass.vcf.gz
-      md5sum: 3076a70abe9c332f3187ac4ac115c198
-    - path: output/artic/test.pass.vcf.gz.tbi
-      md5sum: e7180bb953d2bd657c420a5f76a7164d
-    - path: output/artic/test.preconsensus.fasta
-      md5sum: 12b16397bae7c68d38150571a6ac6185
-    - path: output/artic/test.primers.vcf
-      md5sum: e6e184f1fa153868e3acea0eab42e484
-    - path: output/artic/test.primersitereport.txt
-    - path: output/artic/test.primertrimmed.rg.sorted.bam
-    - path: output/artic/test.primertrimmed.rg.sorted.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/artic/test.sorted.bam
-      md5sum: 199696f431f973c5b6473ddda4089543
-    - path: output/artic/test.sorted.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/artic/test.trimmed.rg.sorted.bam
-    - path: output/artic/test.trimmed.rg.sorted.bam.bai
-      md5sum: 0d76977b2e36046cc176112776c5fa4e
-    - path: output/untar/fast5/100read_fast5/00068f7a-51b3-4933-8fc6-7d6e29181ff9.fast5
-      md5sum: b7aeb3cc877d858f97144d45551264bc
-    - path: output/untar/fast5/100read_fast5/001ed67f-906f-4f37-9770-85d40f5ffee6.fast5
-      md5sum: add9b8658095173f7cef6fc23236d913
-    - path: output/untar/fast5/100read_fast5/0043238c-3a78-48f1-a8ec-d492280da6e4.fast5
-      md5sum: 11d83db48d3b284017b919d476e44294
-    - path: output/untar/fast5/100read_fast5/004a65aa-6700-4ad7-9550-dc59f8708908.fast5
-      md5sum: fb9f124a05af59ea3ede371cd48e404c
-    - path: output/untar/fast5/100read_fast5/00c6481f-9022-4173-9b74-f375c34b9a9b.fast5
-      md5sum: c186053a4fee2d509e1d108be8e131e1
-    - path: output/untar/fast5/100read_fast5/00da3999-12fd-449d-bd07-32a879667a3d.fast5
-      md5sum: ec051e5ce357d632ff740a88087a08fd
-    - path: output/untar/fast5/100read_fast5/018c4b52-48fa-4cc8-a7b4-500f41420279.fast5
-      md5sum: 9d5bae9c9df0105b3b329777977d6f34
-    - path: output/untar/fast5/100read_fast5/01faaaa1-eca2-4bcd-8666-b4d69497107e.fast5
-      md5sum: 5855c80a192a242f03a93b74f12dfa46
-    - path: output/untar/fast5/100read_fast5/02085a68-dc6e-4275-bd1e-f112fed3bd83.fast5
-      md5sum: 6b30e06080aab94b6fa8f476e537f3d2
-    - path: output/untar/fast5/100read_fast5/022647b9-0e16-4318-a794-c5749705b67d.fast5
-      md5sum: 6606f2661a5463772f4ee30a3dba520e
-    - path: output/untar/fast5/100read_fast5/022fc908-aa6e-4d29-a5ad-6a30a9da7e3b.fast5
-      md5sum: 53d611cf6465ef914392c11b88339ba0
-    - path: output/untar/fast5/100read_fast5/02445dc2-39ee-49f1-8a42-51ebfea52c33.fast5
-      md5sum: f7c5844165cbc0566ce1569184fc4213
-    - path: output/untar/fast5/100read_fast5/031ff99b-b11f-40dc-9258-273ec97683f8.fast5
-      md5sum: e78faae6230537a20497d3114cffcafd
-    - path: output/untar/fast5/100read_fast5/03e0e732-cb7a-4084-8fc9-303180c83786.fast5
-      md5sum: 27c8ce19a0955d045053a6925e249ae4
-    - path: output/untar/fast5/100read_fast5/0457184e-6e09-4883-baf3-824d11101c43.fast5
-      md5sum: 7a89c45ae6b360bc585c8b14196ab3f7
-    - path: output/untar/fast5/100read_fast5/045f1e6a-9b5d-4840-bad9-c4b738b61267.fast5
-      md5sum: ee0c3e5fa1f6820968482594f45e8948
-    - path: output/untar/fast5/100read_fast5/046258fa-b951-43a1-bbed-66cdbeac8e71.fast5
-      md5sum: 262d3ee396bab6014505b25ba88cea90
-    - path: output/untar/fast5/100read_fast5/048d5d3a-16ed-4f36-aeb9-3311dd9dc593.fast5
-      md5sum: deea9c03b10aa287f873779baea2a649
-    - path: output/untar/fast5/100read_fast5/04a0ee1e-0406-4394-87ba-a67344318a5d.fast5
-      md5sum: 7f43a0e0de0053a63a28e36374ec20b4
-    - path: output/untar/fast5/100read_fast5/04c07133-cd56-48b9-9f16-86e12cacaf92.fast5
-      md5sum: d607992919072ddb025d766d8ba1a465
-    - path: output/untar/fast5/100read_fast5/052036a3-6af0-4650-9f96-e97e34c52bbc.fast5
-      md5sum: 22ccc03bee288edfc589d5f4b11cb70d
-    - path: output/untar/fast5/100read_fast5/0562aebd-b55b-4752-83eb-12323938c242.fast5
-      md5sum: 1668668f2d0658a6e3417b08ea093c43
-    - path: output/untar/fast5/100read_fast5/0565fd27-4849-4d14-83ff-2864dc3e109e.fast5
-      md5sum: 649ff949e10052b877d9ddb7d6a19009
-    - path: output/untar/fast5/100read_fast5/05f48799-d4ca-4f54-90e2-de208c0c1711.fast5
-      md5sum: 5bddb9c020ddd233adc399c806186af6
-    - path: output/untar/fast5/100read_fast5/064b4a28-a036-46cb-b466-62b8486de288.fast5
-      md5sum: 4f0d1d5400caa14c376c5c2ba5cf4e90
-    - path: output/untar/fast5/100read_fast5/064ef037-67eb-49a4-9a72-e2b2e34cfe5c.fast5
-      md5sum: e8420b20501c06a31223204611aacd44
-    - path: output/untar/fast5/100read_fast5/066c72de-139a-4514-aef9-36cc3927a2c6.fast5
-      md5sum: f703f4942aaa470e2d00706687cea430
-    - path: output/untar/fast5/100read_fast5/069ce6e7-41b9-41b2-a6d8-8d39c16dbaa2.fast5
-      md5sum: 4ef4d47bf346c9cca805e991a6f5400b
-    - path: output/untar/fast5/100read_fast5/06f0339b-75b5-4926-b1a7-878818b5fe67.fast5
-      md5sum: 163a97396e5cf91c40fab7432f52d101
-    - path: output/untar/fast5/100read_fast5/074ebef4-edbd-4d2a-af6c-46512693a990.fast5
-      md5sum: da9798ae314dca12f69ef45c10c8a5a7
-    - path: output/untar/fast5/100read_fast5/08239d1b-1710-4187-b96e-da861a0e4624.fast5
-      md5sum: 8ff2a720e61c52a29e2863d68f84c917
-    - path: output/untar/fast5/100read_fast5/084af0ac-0334-4840-a3a5-3ff62464ae71.fast5
-      md5sum: 3c2f27f6c21eefa53eafaa70252f9f49
-    - path: output/untar/fast5/100read_fast5/08db75dc-49a9-459d-afc8-5ed1d8e47901.fast5
-      md5sum: 6f25bb694f859d53b9dfd4047610d97f
-    - path: output/untar/fast5/100read_fast5/091fba78-028e-4ed2-a799-35e9ba64541c.fast5
-      md5sum: 58da6a195dad9cb15fb5ebb76f9ecd19
-    - path: output/untar/fast5/100read_fast5/094a4c34-c97b-4b83-bd02-1f69e6ccadc0.fast5
-      md5sum: adfb65496a10bae743e3f0e144220b43
-    - path: output/untar/fast5/100read_fast5/09b7f97c-fb32-4a4a-84d9-c45dfc2b46d0.fast5
-      md5sum: fcce7b510edcf012eae95662370d663c
-    - path: output/untar/fast5/100read_fast5/0a30e10c-26b5-4c23-a7ee-493e7b3ebffb.fast5
-      md5sum: fd730b0b9e01a9ce3a0a4f7b39ee838e
-    - path: output/untar/fast5/100read_fast5/0a86654b-30ec-4271-9882-b490de473b5e.fast5
-      md5sum: 9114d618e2713681e7db42932d4b5e92
-    - path: output/untar/fast5/100read_fast5/0a92fbf4-99b4-40cd-98e7-93cfbddeb35e.fast5
-      md5sum: 516a3d935f9cef2abf4eb0a781ba8d19
-    - path: output/untar/fast5/100read_fast5/0af92aee-911c-4402-ba14-ecaabdb73548.fast5
-      md5sum: ccbcd71ecb9a46bd2b657f2e2c11354a
-    - path: output/untar/fast5/100read_fast5/0b168ee0-74c4-494d-a593-a4b4b538a9cb.fast5
-      md5sum: 9f8abf45b60ac800d4195e79bad26ea1
-    - path: output/untar/fast5/100read_fast5/0b8b3929-730d-42a6-84e0-5689b7439c71.fast5
-      md5sum: 1d03a26a58ec0668a1c54cc38fb65c3a
-    - path: output/untar/fast5/100read_fast5/0bb9f17c-3b8f-486d-ac03-6550199a0a49.fast5
-      md5sum: b713ea7f1cd45b5f5041a3a97e87106d
-    - path: output/untar/fast5/100read_fast5/0c5e39bf-e1c5-4208-b110-9a00b55132e4.fast5
-      md5sum: 31e32600bbf9b3523233260868468b00
-    - path: output/untar/fast5/100read_fast5/0cc2613c-9ade-4ec9-96c7-07ab2820bbd7.fast5
-      md5sum: f84eb9bf15a0af603b9f656fb469f305
-    - path: output/untar/fast5/100read_fast5/0cc85c6c-ed86-422e-a093-d2b81089cc6b.fast5
-      md5sum: 536ad1a1c1f8e5c17d8183c7950034a0
-    - path: output/untar/fast5/100read_fast5/0d448640-aa67-4e58-9ce8-004ca23b0412.fast5
-      md5sum: c97a3ae4fcb9123ea4ca89e8a6e391af
-    - path: output/untar/fast5/100read_fast5/0dad8e5f-77e3-4fd1-b569-b06f5b87d8c3.fast5
-      md5sum: 1225db8f9879447708aa85f8a096aafb
-    - path: output/untar/fast5/100read_fast5/0dd4696c-a7dd-4e3a-9ce5-37a258b45373.fast5
-      md5sum: 361426f4430ad8edadae17ab4ddfd7cf
-    - path: output/untar/fast5/100read_fast5/0e5018bc-45fc-40d4-8806-e22e07a915d0.fast5
-      md5sum: f21cba587246cf4c9e0db4f4914db634
-    - path: output/untar/fast5/100read_fast5/0e51c070-d577-4293-8389-bd34fdda9eac.fast5
-      md5sum: e426287a64d0fe356878673c7990e457
-    - path: output/untar/fast5/100read_fast5/0e5ff4de-814b-4ee2-bf8f-3291b8bbdaae.fast5
-      md5sum: a2429274097a3762eb8fd9290208e35d
-    - path: output/untar/fast5/100read_fast5/0f06cd06-1136-4b10-b248-cd4324f6de22.fast5
-      md5sum: 4ddea20115ae9875bff711cb0f2cbcd3
-    - path: output/untar/fast5/100read_fast5/0f3ca011-bb96-4fe2-92e2-31b0bac90d97.fast5
-      md5sum: df29e75d7a273d3b6a75e807a814993a
-    - path: output/untar/fast5/100read_fast5/0f7db51f-ff49-45ea-b58a-9fb58daf249d.fast5
-      md5sum: 671423af2189b08850eaab29b42566ca
-    - path: output/untar/fast5/100read_fast5/0fd3ec80-6fb4-4378-bdb6-df4f84951049.fast5
-      md5sum: 7376ee3f340c041afda6bbd2c3df353f
-    - path: output/untar/fast5/100read_fast5/10361e9b-159a-447d-8cf0-1976515f00f4.fast5
-      md5sum: f73c994cb9b6ec891ea936c54aa2f7a2
-    - path: output/untar/fast5/100read_fast5/10508138-2f5e-4405-99f4-46af4452893c.fast5
-      md5sum: c6a0b38fcd5a4be72793b43149ba04be
-    - path: output/untar/fast5/100read_fast5/10ac42d4-2818-48f6-9d67-1c3019fde890.fast5
-      md5sum: 5e5ae354e0aa8f985f5e5e8bd811eb73
-    - path: output/untar/fast5/100read_fast5/10f98781-e47e-43c3-9006-6d73963ee710.fast5
-      md5sum: 93f6e790fc41c1e266b1c4b18f2ab0ee
-    - path: output/untar/fast5/100read_fast5/1147d9c6-c190-47e6-8007-2e0f18d88f2b.fast5
-      md5sum: 15fbf533ac4a98124cb043abef23d0ba
-    - path: output/untar/fast5/100read_fast5/11e4024c-1997-4372-b1d7-4c884cf58047.fast5
-      md5sum: 788bb232b0b3b059a7f39a72c1f8d1e5
-    - path: output/untar/fast5/100read_fast5/11e944d1-a2c9-409c-ac72-9c1563443df7.fast5
-      md5sum: 31975cf5048b6af550f14b1e217a8f5d
-    - path: output/untar/fast5/100read_fast5/123114b2-247c-4abc-be0c-3a94f02043a2.fast5
-      md5sum: 633689761b59db120dcc5d560587416c
-    - path: output/untar/fast5/100read_fast5/1294c94b-1dac-4c4c-9c36-e8e8996e7f09.fast5
-      md5sum: 161fc1cb25ce05775f81e778f5bb8e93
-    - path: output/untar/fast5/100read_fast5/12ac7997-50bc-4183-95c4-e953ad4eaad1.fast5
-      md5sum: 4a3a4966ede5f0251a65c93c99a66eeb
-    - path: output/untar/fast5/100read_fast5/13265c3e-bbb3-4ebe-b4db-9fbb4bdaff01.fast5
-      md5sum: ad799b6a66cb2d8c08acbf232c23bf49
-    - path: output/untar/fast5/100read_fast5/1377f442-7e38-4c3f-aacb-e8049ad884fe.fast5
-      md5sum: f202ebf7b46bf289b9b1d9e82d8e96db
-    - path: output/untar/fast5/100read_fast5/137cae6b-0009-4ee2-8a0e-7a2e88179c16.fast5
-      md5sum: 6afbc7da1554e1d5328f6e47cc086772
-    - path: output/untar/fast5/100read_fast5/139c8fcc-8dcb-4cf7-aa52-632718587fe7.fast5
-      md5sum: 6aade40bab37e9a4fe008d21732c6790
-    - path: output/untar/fast5/100read_fast5/13bc3b77-a88e-44b9-b119-cd56aa972f61.fast5
-      md5sum: 1d668e59bc724ce47d17f2a4850a9b43
-    - path: output/untar/fast5/100read_fast5/13dbd26f-978f-49ad-9ae6-ca909083b6ce.fast5
-      md5sum: 2106344b03e8b834c20fef4406cf2aa6
-    - path: output/untar/fast5/100read_fast5/151bd13c-c12f-41a6-be02-e97e70a57814.fast5
-      md5sum: 8718a5b883496cde586dbbb256f13bb2
-    - path: output/untar/fast5/100read_fast5/16325928-3440-4a49-94c5-a93b4f6da961.fast5
-      md5sum: da871b8be0d502e05ba6b105f9bd4673
-    - path: output/untar/fast5/100read_fast5/16d9892d-bead-4a6f-b6c5-736c6f602fc1.fast5
-      md5sum: b7844e2a38c120fad74dec350dfd8adf
-    - path: output/untar/fast5/100read_fast5/1721053e-98f4-47a1-ab93-f75bc1c03c79.fast5
-      md5sum: 839e7a9335d54c6dd185a1a9486d9b9e
-    - path: output/untar/fast5/100read_fast5/1730fabf-f1ac-4a02-aa2e-21dcd14fed00.fast5
-      md5sum: ee53b732d0c4dd87dd8742cf4346b311
-    - path: output/untar/fast5/100read_fast5/1783d96c-3955-4405-b765-472c6286be46.fast5
-      md5sum: 6bcbda04b219c8bf971253cc2423a527
-    - path: output/untar/fast5/100read_fast5/180da5c9-4574-48ab-8e6a-8f8a73767e30.fast5
-      md5sum: 8ef4d3255d87a6fb0fa24b621b72e75a
-    - path: output/untar/fast5/100read_fast5/1870a88c-439f-4125-a06c-38b1bf4416e4.fast5
-      md5sum: 62db261bbc152a16b0d910680202ba8a
-    - path: output/untar/fast5/100read_fast5/188b5eae-fce2-439c-b490-aff6c4327499.fast5
-      md5sum: c3157f03f56d03820726ff8ff981b8c9
-    - path: output/untar/fast5/100read_fast5/18cef30b-9fe5-40b4-9094-0389bb5aeb8e.fast5
-      md5sum: 9fc63db9ca59ac6ff6fa15cfe55b3106
-    - path: output/untar/fast5/100read_fast5/18ee103f-1cf8-4694-b2e7-ac228fe70ccd.fast5
-      md5sum: 24dc02b54e6712c583f5977bce1d3cd3
-    - path: output/untar/fast5/100read_fast5/190a9ebe-4d5f-43c0-a495-82ff58944d07.fast5
-      md5sum: 489aa874a1c7c0603076f7ef359d6ace
-    - path: output/untar/fast5/100read_fast5/190c4417-c4cf-40fe-a0df-db4b495a3f77.fast5
-      md5sum: 997a74664ddab756907435890465d554
-    - path: output/untar/fast5/100read_fast5/1a0c9927-e355-49c3-877a-e6b95bc1a402.fast5
-      md5sum: fdc9f5f461d0e30ad29cf84e03b6c18d
-    - path: output/untar/fast5/100read_fast5/1a276f1c-5a5b-4ed2-b071-87f59f7c5233.fast5
-      md5sum: 6269d04009267b7e0df724d7ce355346
-    - path: output/untar/fast5/100read_fast5/1a5c9192-aded-4e94-8dcb-9c04a402978e.fast5
-      md5sum: 78ce5c5d770d7905bc1986203d69ed49
-    - path: output/untar/fast5/100read_fast5/1af84d7e-8fc6-4dba-8750-a0d701f36d1d.fast5
-      md5sum: ed5970f92ecdcce95f84dbb1bd275b8e
-    - path: output/untar/fast5/100read_fast5/1b753736-87b1-4753-ab1d-bfd7e2d94e9e.fast5
-      md5sum: 6b5a2fd8b445d4e43eef6d8597932d88
-    - path: output/untar/fast5/100read_fast5/1b760e8d-7b17-47e0-ba96-5755fc4ddd63.fast5
-      md5sum: 43eb9e8276e9d0870a4c74882d42e5a0
-    - path: output/untar/fast5/100read_fast5/1b86544f-8075-46a2-91f4-baac36216ac2.fast5
-      md5sum: d6266147405391c00aa4dc0ad6797532
-    - path: output/untar/fast5/100read_fast5/1bd0dad7-1600-44a2-90b8-d5cd7b7caa6d.fast5
-      md5sum: 863226172b856834a779eb2013c3a765
-    - path: output/untar/fast5/100read_fast5/1d568051-bdd6-4204-ac34-97b5a3f7375c.fast5
-      md5sum: 7d4cdf29110898e5f6a3288a0a2b9342
-    - path: output/untar/fast5/100read_fast5/1d650a9e-4e67-456a-9abe-bd34b238abe4.fast5
-      md5sum: 3fac1d13ed49703e33e92b8aaab3dac6
-    - path: output/untar/fast5/100read_fast5/1d86c2b3-c2c6-43a1-97ed-8c1f0cbf6476.fast5
-      md5sum: 2eed32c760d94aac2dce49c2364f6cd9
-    - path: output/untar/fast5/100read_fast5/20586d1a-2cd0-45aa-abc2-04ac66d8ea46.fast5
-      md5sum: d89ef1d32a52fc5d45a17d7682e4de22
-    - path: output/untar/fast5/100read_fast5/206626c5-ccf2-4927-9987-164f627bdede.fast5
-      md5sum: 045d9fdb48f0b58456c7012b735c8101
-    - path: output/untar/fast5/100read_fast5/2109d790-67ec-4fd1-8931-6c7e61908ff3.fast5
-      md5sum: 623d2e3213f0423e33b7993d803e4ae5
-    - path: output/untar/fast5/100read_fast5/2166cca5-c0ab-49eb-aec1-fec09bdfbd83.fast5
-      md5sum: 54ac4ec12232104381d2dcd619c9b4be


Reviews:
user: login: SPPearce
body: The nf-test conversion looks good, but the module looks pretty gnarly in its setup.
state: CHANGES_REQUESTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T06:55:56Z
user: login: SPPearce
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T06:56:10Z
user: login: SPPearce
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T06:56:25Z
user: login: LouisLeNezet
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T07:57:36Z
user: login: LouisLeNezet
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T07:57:40Z
user: login: LouisLeNezet
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T07:58:24Z
user: login: LouisLeNezet
state: COMMENTED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T08:28:27Z
user: login: SPPearce
body: Ok, thanks!
state: APPROVED
author_association: CONTRIBUTOR
submitted_at: 2025-03-03T09:27:10Z

Review comments:
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
-    path  sequencing_summary
+    tuple val(meta2), path(model_dir), val(model)
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
path: modules/nf-core/artic/minion/main.nf
user: login: SPPearce
body: What is happening with these two paths, how are they being staged here?
If they really need to be staged into this subfolder then it needs to be set with `stageAs`.
created_at: 2025-03-03T06:55:10Z
author_association: CONTRIBUTOR
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
path: modules/nf-core/artic/minion/main.nf
user: login: SPPearce
body: Where did this go?
created_at: 2025-03-03T06:56:10Z
author_association: CONTRIBUTOR
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
-    path  sequencing_summary
path: modules/nf-core/artic/minion/main.nf
user: login: SPPearce
body: And this?
created_at: 2025-03-03T06:56:25Z
author_association: CONTRIBUTOR
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
path: modules/nf-core/artic/minion/main.nf
user: login: LouisLeNezet
body: The new version of the tool does not use those files
created_at: 2025-03-03T07:57:36Z
author_association: CONTRIBUTOR
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
-    path  sequencing_summary
path: modules/nf-core/artic/minion/main.nf
user: login: LouisLeNezet
body: Same for them
created_at: 2025-03-03T07:57:40Z
author_association: CONTRIBUTOR
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
-    path  sequencing_summary
+    tuple val(meta2), path(model_dir), val(model)
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
path: modules/nf-core/artic/minion/main.nf
user: login: LouisLeNezet
body: Good question, I will update it
created_at: 2025-03-03T07:58:24Z
author_association: CONTRIBUTOR
diff_hunk: @@ -4,17 +4,14 @@ process ARTIC_MINION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/artic:1.2.3--pyhdfd78af_0' :
-        'biocontainers/artic:1.2.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/artic:1.6.1--pyhdfd78af_0' :
+        'biocontainers/artic:1.6.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fastq)
-    path  fast5_dir
-    path  sequencing_summary
+    tuple val(meta2), path(model_dir), val(model)
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
path: modules/nf-core/artic/minion/main.nf
user: login: LouisLeNezet
body: Is it better ?
created_at: 2025-03-03T08:28:27Z
author_association: CONTRIBUTOR

PR comments:
user: login: SPPearce
created_at: 2025-03-03T09:04:35Z
body: That looks much cleaner in the input, shame the tool documentation is so sparse. Where did you find the details of the `--bed` and `--ref` arguments?
author_association: CONTRIBUTOR
user: login: LouisLeNezet
created_at: 2025-03-03T09:09:28Z
body: > That looks much cleaner in the input, shame the tool documentation is so sparse. Where did you find the details of the --bed and --ref arguments?

The problem is that they didn't update their documentation... I went into the [python code](https://github.com/artic-network/fieldbioinformatics/blob/master/artic/minion.py)

And I ran `artic minion --help` in the container

```
usage: artic minion [-h] [-q] [--model MODEL] [--model-dir model_path] [--min-mapq MIN_MAPQ] [--normalise NORMALISE] [--primer-match-threshold PRIMER_MATCH_THRESHOLD]
                    [--min-depth MIN_DEPTH] [--threads THREADS] [--scheme-directory scheme_directory] [--scheme-name scheme_name] [--scheme-length scheme_length]
                    [--scheme-version vX.X.X] [--bed bed] [--ref REF] --read-file read_file [--no-indels] [--no-frameshifts] [--align-consensus] [--dry-run]
                    sample

positional arguments:
  sample                The name of the sample

optional arguments:
  -h, --help            show this help message and exit
  -q, --quiet           Do not output warnings to stderr
  --model MODEL         The model to use for clair3, if not provided the pipeline will try to figure it out the appropriate model from the read fastq
  --model-dir model_path
                        Path containing clair3 models, defaults to models packaged with conda installation (default: $CONDA_PREFIX/bin/models/)
  --min-mapq MIN_MAPQ   Minimum mapping quality to consider (default: 20)
  --normalise NORMALISE
                        Normalise down to moderate coverage to save runtime (default: 100, deactivate with `--normalise 0`)
  --primer-match-threshold PRIMER_MATCH_THRESHOLD
                        Allow fuzzy primer matching within this threshold (default: 35)
  --min-depth MIN_DEPTH
                        Minimum coverage required for a position to be included in the consensus sequence (default: 20)
  --threads THREADS     Number of threads (default: 8)
  --read-file read_file
                        FASTQ file containing reads
  --no-indels           Do not report InDels (uses SNP-only mode of nanopolish/medaka)
  --no-frameshifts      Remove variants which induce frameshifts (ignored when --no-indels set)
  --align-consensus     Run a mafft alignment of consensus to reference after generation
  --dry-run

Remote Scheme Options:
  Options for automagically fetching primer schemes from the scheme repository (https://github.com/quick-lab/primerschemes)

  --scheme-directory scheme_directory
                        Default scheme directory (default: /home/llenezet/repositories/modules/primer-schemes)
  --scheme-name scheme_name
                        Name of the scheme, e.g. sars-cov-2, mpxv to fetch from the scheme repository (https://github.com/quick-lab/primerschemes)
  --scheme-length scheme_length
                        Length of the scheme to fetch from the scheme repository (https://github.com/quick-lab/primerschemes). This is only required if the --scheme-name has
                        multiple possible lengths.
  --scheme-version vX.X.X
                        Primer scheme version

Local Scheme Options:
  Options for providing a local primer scheme and reference sequence (BED file and FASTA file) directly to the pipeline

  --bed bed             BED file containing primer scheme
  --ref REF             Reference sequence for the scheme
```
author_association: CONTRIBUTOR