From d8985998a2a05f5a0431d4137c0ab9992d91f0e8 Mon Sep 17 00:00:00 2001
From: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com>
Date: Mon, 22 Jan 2024 12:30:37 +0100
Subject: [PATCH] Kaiju version bump- nf-test -add stub (#4781)

* kaiju modules patch

* add kaiju nf-test and stub

* adding test & stub 4 kaiju2krona

* undo raven change

* kaiju2table & kaijumkfmi

* Add taxonomic profiling as a keyword in meta.yml
---
 modules/nf-core/kaiju/kaiju/environment.yml   |   2 +-
 modules/nf-core/kaiju/kaiju/main.nf           |  18 ++-
 modules/nf-core/kaiju/kaiju/meta.yml          |   2 +-
 .../nf-core/kaiju/kaiju/tests/main.nf.test    | 117 ++++++++++++++++++
 .../kaiju/kaiju/tests/main.nf.test.snap       |   8 ++
 modules/nf-core/kaiju/kaiju/tests/tags.yml    |   2 +
 .../nf-core/kaiju/kaiju2krona/environment.yml |   2 +-
 modules/nf-core/kaiju/kaiju2krona/main.nf     |  17 ++-
 .../kaiju/kaiju2krona/tests/main.nf.test      | 105 ++++++++++++++++
 .../kaiju/kaiju2krona/tests/main.nf.test.snap |  39 ++++++
 .../nf-core/kaiju/kaiju2krona/tests/tags.yml  |   2 +
 .../nf-core/kaiju/kaiju2table/environment.yml |   2 +-
 modules/nf-core/kaiju/kaiju2table/main.nf     |  24 +++-
 modules/nf-core/kaiju/kaiju2table/meta.yml    |   1 +
 .../kaiju/kaiju2table/tests/main.nf.test      | 106 ++++++++++++++++
 .../kaiju/kaiju2table/tests/main.nf.test.snap |  39 ++++++
 .../nf-core/kaiju/kaiju2table/tests/tags.yml  |   2 +
 modules/nf-core/kaiju/mkfmi/environment.yml   |   7 ++
 modules/nf-core/kaiju/mkfmi/main.nf           |  18 ++-
 .../nf-core/kaiju/mkfmi/tests/main.nf.test    |  58 +++++++++
 .../kaiju/mkfmi/tests/main.nf.test.snap       |  39 ++++++
 .../nf-core/kaiju/mkfmi/tests/nextflow.config |   5 +
 modules/nf-core/kaiju/mkfmi/tests/tags.yml    |   2 +
 tests/config/pytest_modules.yml               |  12 --
 tests/modules/nf-core/kaiju/kaiju/main.nf     |  32 -----
 .../nf-core/kaiju/kaiju/nextflow.config       |   5 -
 tests/modules/nf-core/kaiju/kaiju/test.yml    |  21 ----
 .../modules/nf-core/kaiju/kaiju2krona/main.nf |  20 ---
 .../nf-core/kaiju/kaiju2krona/nextflow.config |   5 -
 .../nf-core/kaiju/kaiju2krona/test.yml        |   8 --
 .../modules/nf-core/kaiju/kaiju2table/main.nf |  21 ----
 .../nf-core/kaiju/kaiju2table/nextflow.config |   5 -
 .../nf-core/kaiju/kaiju2table/test.yml        |   9 --
 tests/modules/nf-core/kaiju/mkfmi/main.nf     |  15 ---
 .../nf-core/kaiju/mkfmi/nextflow.config       |   9 --
 tests/modules/nf-core/kaiju/mkfmi/test.yml    |   9 --
 36 files changed, 600 insertions(+), 188 deletions(-)
 create mode 100644 modules/nf-core/kaiju/kaiju/tests/main.nf.test
 create mode 100644 modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/kaiju/kaiju/tests/tags.yml
 create mode 100644 modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test
 create mode 100644 modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/kaiju/kaiju2krona/tests/tags.yml
 create mode 100644 modules/nf-core/kaiju/kaiju2table/tests/main.nf.test
 create mode 100644 modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/kaiju/kaiju2table/tests/tags.yml
 create mode 100644 modules/nf-core/kaiju/mkfmi/environment.yml
 create mode 100644 modules/nf-core/kaiju/mkfmi/tests/main.nf.test
 create mode 100644 modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/kaiju/mkfmi/tests/nextflow.config
 create mode 100644 modules/nf-core/kaiju/mkfmi/tests/tags.yml
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju/main.nf
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju/nextflow.config
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju/test.yml
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju2krona/main.nf
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju2krona/test.yml
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju2table/main.nf
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju2table/nextflow.config
 delete mode 100644 tests/modules/nf-core/kaiju/kaiju2table/test.yml
 delete mode 100644 tests/modules/nf-core/kaiju/mkfmi/main.nf
 delete mode 100644 tests/modules/nf-core/kaiju/mkfmi/nextflow.config
 delete mode 100644 tests/modules/nf-core/kaiju/mkfmi/test.yml

diff --git a/modules/nf-core/kaiju/kaiju/environment.yml b/modules/nf-core/kaiju/kaiju/environment.yml
index dd491adb36be..baac450b265f 100644
--- a/modules/nf-core/kaiju/kaiju/environment.yml
+++ b/modules/nf-core/kaiju/kaiju/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kaiju=1.8.2
+  - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/kaiju/main.nf b/modules/nf-core/kaiju/kaiju/main.nf
index 308048a86e85..2f5f6e7d8c9d 100644
--- a/modules/nf-core/kaiju/kaiju/main.nf
+++ b/modules/nf-core/kaiju/kaiju/main.nf
@@ -4,8 +4,8 @@ process KAIJU_KAIJU {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -38,4 +38,18 @@ process KAIJU_KAIJU {
         kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/kaiju/kaiju/meta.yml b/modules/nf-core/kaiju/kaiju/meta.yml
index 7a6840fedede..33c85690757f 100644
--- a/modules/nf-core/kaiju/kaiju/meta.yml
+++ b/modules/nf-core/kaiju/kaiju/meta.yml
@@ -26,7 +26,7 @@ input:
         respectively.
       pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}"
   - db:
-      type: files
+      type: directory
       description: |
         List containing the database and nodes files for Kaiju
         e.g. [ 'database.fmi', 'nodes.dmp' ]
diff --git a/modules/nf-core/kaiju/kaiju/tests/main.nf.test b/modules/nf-core/kaiju/kaiju/tests/main.nf.test
new file mode 100644
index 000000000000..ede2f9525219
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/tests/main.nf.test
@@ -0,0 +1,117 @@
+nextflow_process {
+
+    name "Test Process KAIJU_KAIJU"
+    script "../main.nf"
+    process "KAIJU_KAIJU"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kaiju"
+    tag "kaiju/kaiju"
+    tag "untar"
+
+    test("sarscov2 - fastq - single-end") {
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] =  [
+                        [ id:'test', single_end:true ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                        ]
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.results[0][1]).getText().contains("C\tERR5069949.2257580\t2697049") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq - paired-end") {
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ]
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.results[0][1]).getText().contains("C\tERR5069949.2257580\t2697049") }
+            )
+        }
+    }
+
+    test("sarscov2 - fastq - stub") {
+
+        options '-stub'
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)]
+                ]
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.results[0][1]).name).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap b/modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap
new file mode 100644
index 000000000000..08735f477b64
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/tests/main.nf.test.snap
@@ -0,0 +1,8 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            "test.tsv"
+        ],
+        "timestamp": "2024-01-20T14:44:57.116024519"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kaiju/kaiju/tests/tags.yml b/modules/nf-core/kaiju/kaiju/tests/tags.yml
new file mode 100644
index 000000000000..c73d4df5cb28
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/kaiju:
+  - "modules/nf-core/kaiju/kaiju/**"
diff --git a/modules/nf-core/kaiju/kaiju2krona/environment.yml b/modules/nf-core/kaiju/kaiju2krona/environment.yml
index f3d27c307b0d..2905be97f692 100644
--- a/modules/nf-core/kaiju/kaiju2krona/environment.yml
+++ b/modules/nf-core/kaiju/kaiju2krona/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kaiju=1.8.2
+  - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/kaiju2krona/main.nf b/modules/nf-core/kaiju/kaiju2krona/main.nf
index 86d596de68b9..85d2dfd2a7bc 100644
--- a/modules/nf-core/kaiju/kaiju2krona/main.nf
+++ b/modules/nf-core/kaiju/kaiju2krona/main.nf
@@ -4,8 +4,8 @@ process KAIJU_KAIJU2KRONA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -36,4 +36,17 @@ process KAIJU_KAIJU2KRONA {
         kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
 }
+
diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test
new file mode 100644
index 000000000000..cf522cd0fa28
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test
@@ -0,0 +1,105 @@
+nextflow_process {
+
+    name "Test Process KAIJU_KAIJU2KRONA"
+    script "../main.nf"
+    process "KAIJU_KAIJU2KRONA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kaiju"
+    tag "kaiju/kaiju2krona"
+    tag "kaiju/kaiju"
+    tag "untar"
+
+    test("sarscov2 - fastq - single-end") {
+
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+
+            run("KAIJU_KAIJU") {
+                script "../../kaiju/main.nf"
+                process {
+                    """
+                    input[0] =  [
+                            [ id:'test', single_end:true ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+        }
+
+            when {
+                process {
+                    """
+                    input[0] = KAIJU_KAIJU.out.results
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+
+            then {
+                assertAll(
+                    { assert process.success },
+                    { assert snapshot(process.out).match() }
+                )
+            }
+
+    }
+
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+
+            run("KAIJU_KAIJU") {
+                script "../../kaiju/main.nf"
+                process {
+                    """
+                    input[0] =  [
+                            [ id:'test', single_end:true ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = KAIJU_KAIJU.out.results
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.txt[0][1]).name).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap
new file mode 100644
index 000000000000..5532a6948cab
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test.snap
@@ -0,0 +1,39 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            "test.txt"
+        ],
+        "timestamp": "2024-01-20T15:06:32.789121011"
+    },
+    "sarscov2 - fastq - single-end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.txt:md5,68b2309d37767e444193fa6cea7c0494"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f75aa349971d581981d3a0399450b395"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.txt:md5,68b2309d37767e444193fa6cea7c0494"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f75aa349971d581981d3a0399450b395"
+                ]
+            }
+        ],
+        "timestamp": "2024-01-20T15:06:08.840865115"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kaiju/kaiju2krona/tests/tags.yml b/modules/nf-core/kaiju/kaiju2krona/tests/tags.yml
new file mode 100644
index 000000000000..661fe924da1d
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2krona/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/kaiju2krona:
+  - "modules/nf-core/kaiju/kaiju2krona/**"
diff --git a/modules/nf-core/kaiju/kaiju2table/environment.yml b/modules/nf-core/kaiju/kaiju2table/environment.yml
index 81a6ca0bc0d2..18685f415760 100644
--- a/modules/nf-core/kaiju/kaiju2table/environment.yml
+++ b/modules/nf-core/kaiju/kaiju2table/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kaiju=1.8.2
+  - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/kaiju2table/main.nf b/modules/nf-core/kaiju/kaiju2table/main.nf
index 173e2bb12ed5..44049744ada6 100644
--- a/modules/nf-core/kaiju/kaiju2table/main.nf
+++ b/modules/nf-core/kaiju/kaiju2table/main.nf
@@ -4,11 +4,11 @@ process KAIJU_KAIJU2TABLE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'biocontainers/kaiju:1.8.2--h2e03b76_0' }"
+        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
 
     input:
-    tuple val(meta), path(results)
+    tuple val(meta), path(input)
     path db
     val taxon_rank
 
@@ -24,13 +24,25 @@ process KAIJU_KAIJU2TABLE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     dbnodes=`find -L ${db} -name "*nodes.dmp"`
-    dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
+    dbnames=`find -L ${db} -name "*names.dmp"`
     kaiju2table   $args \\
         -t \$dbnodes \\
-        -n \$dbname \\
+        -n \$dbnames \\
         -r ${taxon_rank} \\
         -o ${prefix}.txt \\
-        ${results}
+        ${input}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/kaiju/kaiju2table/meta.yml b/modules/nf-core/kaiju/kaiju2table/meta.yml
index 077e82de6e8d..0f62374e8c5c 100644
--- a/modules/nf-core/kaiju/kaiju2table/meta.yml
+++ b/modules/nf-core/kaiju/kaiju2table/meta.yml
@@ -3,6 +3,7 @@ description: write your description here
 keywords:
   - classify
   - metagenomics
+  - taxonomic profiling
 tools:
   - kaiju:
       description: Fast and sensitive taxonomic classification for metagenomics
diff --git a/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test
new file mode 100644
index 000000000000..d93fb31ac414
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test
@@ -0,0 +1,106 @@
+nextflow_process {
+
+    name "Test Process KAIJU_KAIJU2TABLE"
+    script "../main.nf"
+    process "KAIJU_KAIJU2TABLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kaiju"
+    tag "kaiju/kaiju2table"
+    tag "kaiju/kaiju"
+    tag "untar"
+
+    test("sarscov2 - fastq - single-end") {
+
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+
+            run("KAIJU_KAIJU") {
+                script "../../kaiju/main.nf"
+                process {
+                    """
+                    input[0] =  [
+                            [ id:'test', single_end:true ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+        }
+
+            when {
+                process {
+                    """
+                    input[0] = KAIJU_KAIJU.out.results
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    input[2] = 'species'
+                    """
+                }
+            }
+
+            then {
+                assertAll(
+                    { assert process.success },
+                    { assert snapshot(process.out).match() }
+                )
+            }
+
+    }
+
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+
+            run("KAIJU_KAIJU") {
+                script "../../kaiju/main.nf"
+                process {
+                    """
+                    input[0] =  [
+                            [ id:'test', single_end:true ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
+                            ]
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = KAIJU_KAIJU.out.results
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                input[2] = 'species'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.summary[0][1]).name).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap
new file mode 100644
index 000000000000..e97eb8b88040
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/tests/main.nf.test.snap
@@ -0,0 +1,39 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            "test.txt"
+        ],
+        "timestamp": "2024-01-20T16:10:49.521322767"
+    },
+    "sarscov2 - fastq - single-end": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.txt:md5,0d9f8fd36fcf2888296ae12632c5f0a8"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2b2b98cb635a611e5eb964e5a77f6248"
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.txt:md5,0d9f8fd36fcf2888296ae12632c5f0a8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2b2b98cb635a611e5eb964e5a77f6248"
+                ]
+            }
+        ],
+        "timestamp": "2024-01-20T16:08:47.644443775"
+    }
+}
diff --git a/modules/nf-core/kaiju/kaiju2table/tests/tags.yml b/modules/nf-core/kaiju/kaiju2table/tests/tags.yml
new file mode 100644
index 000000000000..0fa6b81e7368
--- /dev/null
+++ b/modules/nf-core/kaiju/kaiju2table/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/kaiju2table:
+  - "modules/nf-core/kaiju/kaiju2table/**"
diff --git a/modules/nf-core/kaiju/mkfmi/environment.yml b/modules/nf-core/kaiju/mkfmi/environment.yml
new file mode 100644
index 000000000000..9b66ea1eaa1f
--- /dev/null
+++ b/modules/nf-core/kaiju/mkfmi/environment.yml
@@ -0,0 +1,7 @@
+name: kaiju_mkfmi
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::kaiju=1.10.0
diff --git a/modules/nf-core/kaiju/mkfmi/main.nf b/modules/nf-core/kaiju/mkfmi/main.nf
index bd9bad6abaa2..d08be63bb5e7 100644
--- a/modules/nf-core/kaiju/mkfmi/main.nf
+++ b/modules/nf-core/kaiju/mkfmi/main.nf
@@ -2,10 +2,10 @@ process KAIJU_MKFMI {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::kaiju=1.9.2"
+    conda "bioconda::kaiju=1.10.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.9.2--h5b5514e_0':
-        'biocontainers/kaiju:1.9.2--h5b5514e_0' }"
+        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -33,4 +33,16 @@ process KAIJU_MKFMI {
         kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fmi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test
new file mode 100644
index 000000000000..d8062b0b9f92
--- /dev/null
+++ b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test
@@ -0,0 +1,58 @@
+nextflow_process {
+
+    name "Test Process KAIJU_MKFMI"
+    script "../main.nf"
+    process "KAIJU_MKFMI"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kaiju"
+    tag "kaiju/mkfmi"
+
+    test("sarscov2 - proteome - fasta") {
+
+        when {
+            process {
+                """
+                input[0] =  [
+                        [ id:'test', single_end:true ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] =  [
+                        [ id:'test', single_end:true ],
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.fmi[0][1]).name).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap
new file mode 100644
index 000000000000..9120a164e4f3
--- /dev/null
+++ b/modules/nf-core/kaiju/mkfmi/tests/main.nf.test.snap
@@ -0,0 +1,39 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            "test.fmi"
+        ],
+        "timestamp": "2024-01-20T16:27:00.670884904"
+    },
+    "sarscov2 - proteome - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fmi:md5,54fd89f5e4eab61af30175e8aa389598"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3cbd427d0187ffee188347830d33dc12"
+                ],
+                "fmi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.fmi:md5,54fd89f5e4eab61af30175e8aa389598"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3cbd427d0187ffee188347830d33dc12"
+                ]
+            }
+        ],
+        "timestamp": "2024-01-20T16:26:48.062489887"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kaiju/mkfmi/tests/nextflow.config b/modules/nf-core/kaiju/mkfmi/tests/nextflow.config
new file mode 100644
index 000000000000..ae99671ff4b3
--- /dev/null
+++ b/modules/nf-core/kaiju/mkfmi/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: KAIJU_MKFMI {
+        ext.args = '-a ACDEFGHIKLMNPQRSTVWY'
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/kaiju/mkfmi/tests/tags.yml b/modules/nf-core/kaiju/mkfmi/tests/tags.yml
new file mode 100644
index 000000000000..ee1305f23f1c
--- /dev/null
+++ b/modules/nf-core/kaiju/mkfmi/tests/tags.yml
@@ -0,0 +1,2 @@
+kaiju/mkfmi:
+  - "modules/nf-core/kaiju/mkfmi/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 0dbe8e17ab45..36554980c9ab 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1245,18 +1245,6 @@ jasminesv:
 jupyternotebook:
   - modules/nf-core/jupyternotebook/**
   - tests/modules/nf-core/jupyternotebook/**
-kaiju/kaiju:
-  - modules/nf-core/kaiju/kaiju/**
-  - tests/modules/nf-core/kaiju/kaiju/**
-kaiju/kaiju2krona:
-  - modules/nf-core/kaiju/kaiju2krona/**
-  - tests/modules/nf-core/kaiju/kaiju2krona/**
-kaiju/kaiju2table:
-  - modules/nf-core/kaiju/kaiju2table/**
-  - tests/modules/nf-core/kaiju/kaiju2table/**
-kaiju/mkfmi:
-  - modules/nf-core/kaiju/mkfmi/**
-  - tests/modules/nf-core/kaiju/mkfmi/**
 kallistobustools/count:
   - modules/nf-core/kallistobustools/count/**
   - tests/modules/nf-core/kallistobustools/count/**
diff --git a/tests/modules/nf-core/kaiju/kaiju/main.nf b/tests/modules/nf-core/kaiju/kaiju/main.nf
deleted file mode 100644
index c2b1d60e7121..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju/main.nf
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR       } from '../../../../../modules/nf-core/untar/main.nf'
-include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf'
-
-workflow test_kaiju_kaiju_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
-}
-
-workflow test_kaiju_kaiju_paired_end {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-    ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
-
-}
diff --git a/tests/modules/nf-core/kaiju/kaiju/nextflow.config b/tests/modules/nf-core/kaiju/kaiju/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/kaiju/kaiju/test.yml b/tests/modules/nf-core/kaiju/kaiju/test.yml
deleted file mode 100644
index 9e495ede0b05..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: kaiju kaiju test_kaiju_kaiju_single_end
-  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_single_end -c ./tests/config/nextflow.config
-  tags:
-    - kaiju/kaiju
-    - kaiju
-  files:
-    - path: output/kaiju/test.tsv
-      contains: ["C\tERR5069949.2257580\t2697049"]
-    - path: output/kaiju/versions.yml
-      md5sum: 7e218c0ea00a71dd3a5ec5aaf28804f4
-
-- name: kaiju kaiju test_kaiju_kaiju_paired_end
-  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju -entry test_kaiju_kaiju_paired_end -c ./tests/config/nextflow.config
-  tags:
-    - kaiju/kaiju
-    - kaiju
-  files:
-    - path: output/kaiju/test.tsv
-      contains: ["C\tERR5069949.2257580\t2697049"]
-    - path: output/kaiju/versions.yml
-      md5sum: a74215f6f69979ae046fb1d65c56ac67
diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf b/tests/modules/nf-core/kaiju/kaiju2krona/main.nf
deleted file mode 100644
index 62adf390caf5..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju2krona/main.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR } from '../../../../../modules/nf-core/untar/main.nf'
-include { KAIJU_KAIJU } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf'
-include { KAIJU_KAIJU2KRONA } from '../../../../../modules/nf-core/kaiju/kaiju2krona/main.nf'
-
-workflow test_kaiju_kaiju2krona {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-
-    UNTAR ( db )
-    KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
-    KAIJU_KAIJU2KRONA ( KAIJU_KAIJU.out.results , UNTAR.out.untar.map{ it[1] } )
-}
diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config b/tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/kaiju/kaiju2krona/test.yml b/tests/modules/nf-core/kaiju/kaiju2krona/test.yml
deleted file mode 100644
index 1dcf0565645d..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju2krona/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: kaiju kaiju2krona test_kaiju_kaiju2krona
-  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju2krona -entry test_kaiju_kaiju2krona -c ./tests/config/nextflow.config  -c ./tests/modules/nf-core/kaiju/kaiju2krona/nextflow.config
-  tags:
-    - kaiju/kaiju2krona
-    - kaiju
-  files:
-    - path: output/kaiju/test.txt
-      md5sum: 68b2309d37767e444193fa6cea7c0494
diff --git a/tests/modules/nf-core/kaiju/kaiju2table/main.nf b/tests/modules/nf-core/kaiju/kaiju2table/main.nf
deleted file mode 100644
index 413a7b39a930..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju2table/main.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { UNTAR             } from '../../../../../modules/nf-core/untar/main.nf'
-include { KAIJU_KAIJU       } from '../../../../../modules/nf-core/kaiju/kaiju/main.nf'
-include { KAIJU_KAIJU2TABLE } from '../../../../../modules/nf-core/kaiju/kaiju2table/main.nf'
-
-workflow test_kaiju_kaiju_single_end {
-
-    input = [
-        [ id:'test', single_end:true ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
-    ]
-    db    = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
-    taxon_rank = "species"
-
-    ch_db = UNTAR ( db )
-    KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
-    KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
-}
diff --git a/tests/modules/nf-core/kaiju/kaiju2table/nextflow.config b/tests/modules/nf-core/kaiju/kaiju2table/nextflow.config
deleted file mode 100644
index 50f50a7a3579..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju2table/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/kaiju/kaiju2table/test.yml b/tests/modules/nf-core/kaiju/kaiju2table/test.yml
deleted file mode 100644
index aeb1fd57d753..000000000000
--- a/tests/modules/nf-core/kaiju/kaiju2table/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: kaiju kaiju2table test_kaiju_kaiju_single_end
-  command: nextflow run ./tests/modules/nf-core/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c ./tests/config/nextflow.config
-  tags:
-    - kaiju
-    - kaiju/kaiju2table
-  files:
-    - path: output/kaiju/test.txt
-      md5sum: 0d9f8fd36fcf2888296ae12632c5f0a8
-    - path: output/kaiju/versions.yml
diff --git a/tests/modules/nf-core/kaiju/mkfmi/main.nf b/tests/modules/nf-core/kaiju/mkfmi/main.nf
deleted file mode 100644
index 488268969c1f..000000000000
--- a/tests/modules/nf-core/kaiju/mkfmi/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { KAIJU_MKFMI } from '../../../../../modules/nf-core/kaiju/mkfmi/main.nf'
-
-workflow test_kaiju_mkfmi {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true)
-    ]
-
-    KAIJU_MKFMI ( input )
-}
diff --git a/tests/modules/nf-core/kaiju/mkfmi/nextflow.config b/tests/modules/nf-core/kaiju/mkfmi/nextflow.config
deleted file mode 100644
index cfcf98872bc6..000000000000
--- a/tests/modules/nf-core/kaiju/mkfmi/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: KAIJU_MKFMI {
-        ext.args = '-a ACDEFGHIKLMNPQRSTVWY'
-    }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/kaiju/mkfmi/test.yml b/tests/modules/nf-core/kaiju/mkfmi/test.yml
deleted file mode 100644
index 8c44efce1af0..000000000000
--- a/tests/modules/nf-core/kaiju/mkfmi/test.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-- name: kaiju mkfmi test_kaiju_mkfmi
-  command: nextflow run ./tests/modules/nf-core/kaiju/mkfmi -entry test_kaiju_mkfmi -c ./tests/config/nextflow.config
-  tags:
-    - kaiju/mkfmi
-    - kaiju
-  files:
-    - path: output/kaiju/test.fmi
-      md5sum: 05615794180a9c2e739a9bf1c24c99d5
-    - path: output/kaiju/versions.yml