diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d2fa6e12..44d5d5b2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -97,18 +97,14 @@ jobs:
     strategy:
       matrix:
         # Run remaining test profiles with minimum nextflow version
-        test_name:
-          [
-            test_host_rm,
-            test_hybrid,
-            test_hybrid_host_rm,
-            test_busco_auto,
-            test_ancient_dna,
-            test_adapterremoval,
-            test_binrefinement,
-            test_virus_identification,
+        profile: [
+            test_nothing, ## fast config to kill all other jobs if something fundamentally wrong
             test_single_end,
-            test_concoct,
+            test_alternatives,
+            test_preassembly_binrefine, ## TODO CHE KOUTPUT
+            test_hybrid_host_rm,
+            #test_extras,
+            #test_bigdb,
           ]
     steps:
       - name: Free some space
@@ -129,37 +125,4 @@ jobs:
 
       - name: Run pipeline with ${{ matrix.test_name }} test profile
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},docker --outdir ./results
-
-  checkm:
-    name: Run single test to checkm due to database download
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Free some space
-        run: |
-          sudo rm -rf "/usr/local/share/boost"
-          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-
-      - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-
-      - name: Install Nextflow
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - name: Download and prepare CheckM database
-        run: |
-          mkdir -p databases/checkm
-          wget https://zenodo.org/records/7401545/files/checkm_data_2015_01_16.tar.gz -P databases/checkm
-          tar xzvf databases/checkm/checkm_data_2015_01_16.tar.gz -C databases/checkm/
-
-      - name: Run pipeline with ${{ matrix.profile }} test profile
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --binqc_tool checkm --checkm_db databases/checkm
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results
diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config
deleted file mode 100644
index 63f04cf6..00000000
--- a/conf/test_adapterremoval.config
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-// Limit resources so that this can run on GitHub Actions
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
-params {
-    config_profile_name         = 'Test profile for running with AdapterRemoval and domain classification'
-    config_profile_description  = 'Minimal test dataset to check pipeline function with AdapterRemoval data and domain classification.'
-
-    // Input data
-    input                       = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.euk.csv'
-    centrifuge_db               = params.pipelines_testdata_base_path + 'mag/test_data/minigut_cf.tar.gz'
-    kraken2_db                  = params.pipelines_testdata_base_path + 'mag/test_data/minigut_kraken.tgz'
-    metaeuk_db                  = params.pipelines_testdata_base_path + '/modules/data/proteomics/database/yeast_UPS.fasta'
-    skip_krona                  = true
-    min_length_unbinned_contigs = 1
-    max_unbinned_contigs        = 2
-    busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
-    skip_gtdbtk                 = true
-    gtdbtk_min_completeness     = 0.01
-    clip_tool                   = 'adapterremoval'
-    skip_concoct                = true
-    bin_domain_classification   = true
-}
diff --git a/conf/test_bbnorm.config b/conf/test_alternatives.config
similarity index 60%
rename from conf/test_bbnorm.config
rename to conf/test_alternatives.config
index 223f99a3..99b32ee9 100644
--- a/conf/test_bbnorm.config
+++ b/conf/test_alternatives.config
@@ -1,11 +1,12 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
+    Nextflow config file for running minimal tests of alternative tools from default
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
+    Defines input files and everything required to run a fast and simple pipeline test
+    of all alternative tools from a default test run.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/mag -profile test_alternatives,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -21,25 +22,23 @@ process {
 
 params {
     config_profile_name         = 'Test profile'
-    config_profile_description  = 'Minimal test dataset to check pipeline function'
+    config_profile_description  = 'Minimal test dataset with alternative tools to check pipeline function'
 
-    // Input data
-    input                       = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.csv'
-    keep_phix                   = true
-    skip_clipping               = true
-    skip_prokka                 = true
-    skip_prodigal               = true
-    skip_quast                  = true
-    skip_binning                = true
+    // Input data -> Defaults
+    input                       = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.multirun.csv'
     centrifuge_db               = params.pipelines_testdata_base_path + 'mag/test_data/minigut_cf.tar.gz'
     kraken2_db                  = params.pipelines_testdata_base_path + 'mag/test_data/minigut_kraken.tgz'
-    skip_krona                  = true
+    skip_krona                  = false
     min_length_unbinned_contigs = 1
     max_unbinned_contigs        = 2
     busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
     busco_clean                 = true
     skip_gtdbtk                 = true
-    gtdbtk_min_completeness     = 0.01
-    bbnorm                      = true
-    coassemble_group            = true
+    gtdbtk_min_completeness     = 0
+    skip_concoct                = true
+
+    // Alternate tools from default test
+    clip_tool                   = 'adapterremoval'
+    binqc_tool                  = 'checkm'
+    bin_domain_classification   = true
 }
diff --git a/conf/test_ancient_dna.config b/conf/test_ancient_dna.config
deleted file mode 100644
index e8dab425..00000000
--- a/conf/test_ancient_dna.config
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/mag -profile test_ancient_dna,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-// Limit resources so that this can run on GitHub Actions
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
-
-params {
-    config_profile_name                  = 'Ancient DNA test profile '
-    config_profile_description           = 'Minimal test dataset to check pipeline function for ancient DNA step'
-
-    // Input data
-    input                                = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.csv'
-    centrifuge_db                        = params.pipelines_testdata_base_path + 'mag/test_data/minigut_cf.tar.gz'
-    kraken2_db                           = params.pipelines_testdata_base_path + 'mag/test_data/minigut_kraken.tgz'
-    skip_krona                           = true
-    min_length_unbinned_contigs          = 1
-    max_unbinned_contigs                 = 2
-    busco_db                             = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
-    skip_gtdbtk                          = true
-    gtdbtk_min_completeness              = 0.01
-    ancient_dna                          = true
-    binning_map_mode                     = 'own'
-    skip_spades                          = false
-    skip_spadeshybrid                    = true
-    bcftools_view_high_variant_quality   = 0
-    bcftools_view_medium_variant_quality = 0
-    bcftools_view_minimal_allelesupport  = 3
-    refine_bins_dastool                  = true
-    refine_bins_dastool_threshold        = 0
-    skip_concoct                         = true
-}
diff --git a/conf/test_bigdb.config b/conf/test_bigdb.config
new file mode 100644
index 00000000..e69de29b
diff --git a/conf/test_concoct.config b/conf/test_concoct.config
deleted file mode 100644
index 2d90ab50..00000000
--- a/conf/test_concoct.config
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Runs input data but skipping all possible steps to allow for a fast testing
-    profile for input checks etc.
-
-    Use as follows:
-        nextflow run nf-core/mag -profile test_nothing,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-// Limit resources so that this can run on GitHub Actions
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
-params {
-    config_profile_name        = 'Test CONCOCT profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
-
-    // Input data
-    input                      = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.csv'
-    centrifuge_db              = null
-    kraken2_db                 = null
-    skip_krona                 = true
-    skip_clipping              = true
-    skip_adapter_trimming      = false
-    skip_spades                = true
-    skip_spadeshybrid          = true
-    skip_megahit               = false
-    skip_quast                 = true
-    skip_prodigal              = true
-    skip_binning               = false
-    skip_metabat2              = false
-    skip_maxbin2               = true
-    skip_concoct               = false
-    skip_prokka                = true
-    skip_binqc                 = true
-    skip_gtdbtk                = true
-    gtdbtk_min_completeness    = 0.01
-}
diff --git a/conf/test_extras.config b/conf/test_extras.config
new file mode 100644
index 00000000..e69de29b
diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config
deleted file mode 100644
index e241e03e..00000000
--- a/conf/test_host_rm.config
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/mag -profile test_host_rm,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-// Limit resources so that this can run on GitHub Actions
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
-params {
-    config_profile_name         = 'Test profile'
-    config_profile_description  = 'Minimal test dataset to check pipeline function'
-
-    // Input data
-    host_fasta                  = params.pipelines_testdata_base_path + 'mag/host_reference/genome.hg38.chr21_10000bp_region.fa'
-    input                       = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.host_rm.csv'
-    min_length_unbinned_contigs = 1
-    max_unbinned_contigs        = 2
-    busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
-    skip_gtdbtk                 = true
-    gtdbtk_min_completeness     = 0.01
-    skip_concoct                = true
-}
diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config
deleted file mode 100644
index cfb0991c..00000000
--- a/conf/test_hybrid.config
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/mag -profile test_hybrid,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-// Limit resources so that this can run on GitHub Actions
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
-params {
-    config_profile_name         = 'Test profile'
-    config_profile_description  = 'Minimal test dataset to check pipeline function'
-
-    // Input data
-    input                       = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.hybrid.csv'
-    min_length_unbinned_contigs = 1
-    max_unbinned_contigs        = 2
-    busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
-    skip_gtdbtk                 = true
-    gtdbtk_min_completeness     = 0.01
-    skip_concoct                = true
-}
diff --git a/conf/test_binrefinement.config b/conf/test_preassembly_binrefine.config
similarity index 78%
rename from conf/test_binrefinement.config
rename to conf/test_preassembly_binrefine.config
index 9602197c..447e53b7 100644
--- a/conf/test_binrefinement.config
+++ b/conf/test_preassembly_binrefine.config
@@ -26,17 +26,22 @@ params {
     // Input data
     input                         = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.csv'
     assembly_input                = params.pipelines_testdata_base_path + 'mag/samplesheets/assembly_samplesheet.csv'
-    centrifuge_db                 = params.pipelines_testdata_base_path + 'mag/test_data/minigut_cf.tar.gz'
-    kraken2_db                    = params.pipelines_testdata_base_path + 'mag/test_data/minigut_kraken.tgz'
     skip_krona                    = true
     min_length_unbinned_contigs   = 1
     max_unbinned_contigs          = 2
+    skip_metaeuk                  = false
+    metaeuk_db                    = 'https://github.com/nf-core/test-datasets/raw/modules/data/proteomics/database/yeast_UPS.fasta'
+    run_virus_identification      = true
+    genomad_splits                = 4
     busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2024-01-08.tar.gz"
     skip_gtdbtk                   = true
     gtdbtk_min_completeness       = 0.01
     refine_bins_dastool           = true
     refine_bins_dastool_threshold = 0
-    // TODO not using 'both' until #489 merged
     postbinning_input             = 'refined_bins_only'
     busco_clean                   = true
+    run_gunc                      = true
+
+    // For runtime reasons
+    skip_prokka = true // CONCOCT makes hundreds of bins, and Prokka is slow (keeping on runs for 28m, without 22m),
 }
diff --git a/conf/test_single_end.config b/conf/test_single_end.config
index 951a4361..2501d47a 100644
--- a/conf/test_single_end.config
+++ b/conf/test_single_end.config
@@ -33,7 +33,6 @@ params {
     binning_map_mode            = 'own'
     min_length_unbinned_contigs = 1000000
     max_unbinned_contigs        = 2
-    skip_gtdbtk                 = true
     skip_concoct                = true
     skip_binqc                  = true
     skip_gtdbtk                 = true
diff --git a/conf/test_virus_identification.config b/conf/test_virus_identification.config
deleted file mode 100644
index 380401b3..00000000
--- a/conf/test_virus_identification.config
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
-========================================================================================
-    Nextflow config file for running minimal tests
-========================================================================================
-    Defines input files and everything required to run a fast and simple pipeline test.
-
-    Use as follows:
-        nextflow run nf-core/mag -profile test_virus_identification,<docker/singularity> --outdir <OUTDIR>
-
-----------------------------------------------------------------------------------------
-*/
-
-// Limit resources so that this can run on GitHub Actions
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
-params {
-    config_profile_name        = 'Test profile for running virus_identification'
-    config_profile_description = 'Minimal test dataset to check pipeline function virus identification'
-
-    // Input data
-    input                      = params.pipelines_testdata_base_path + 'mag/samplesheets/samplesheet.csv'
-    run_virus_identification   = true
-    genomad_splits             = 7
-
-    // For computational efficiency
-    reads_minlength            = 150
-    coassemble_group           = true
-    skip_gtdbtk                = true
-    gtdbtk_min_completeness    = 0.01
-    skip_binning               = true
-    skip_prokka                = true
-    skip_spades                = true
-    skip_spadeshybrid          = true
-    skip_quast                 = true
-    skip_prodigal              = true
-    skip_krona                 = true
-    skip_adapter_trimming      = true
-    skip_metabat2              = true
-    skip_maxbin2               = true
-    skip_busco                 = true
-}
diff --git a/modules.json b/modules.json
index d56420d0..766edb40 100644
--- a/modules.json
+++ b/modules.json
@@ -239,7 +239,7 @@
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031",
                         "installed_by": ["modules"]
                     },
                     "pydamage/analyze": {
diff --git a/modules/nf-core/prokka/environment.yml b/modules/nf-core/prokka/environment.yml
new file mode 100644
index 00000000..d7c44d5a
--- /dev/null
+++ b/modules/nf-core/prokka/environment.yml
@@ -0,0 +1,7 @@
+name: prokka
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::prokka=1.14.6
diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf
index 60fbe232..adfda037 100644
--- a/modules/nf-core/prokka/main.nf
+++ b/modules/nf-core/prokka/main.nf
@@ -2,9 +2,9 @@ process PROKKA {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::prokka=1.14.6"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' :
+        'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' :
         'biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
 
     input:
diff --git a/modules/nf-core/prokka/meta.yml b/modules/nf-core/prokka/meta.yml
index 7fc9e185..9d82ffac 100644
--- a/modules/nf-core/prokka/meta.yml
+++ b/modules/nf-core/prokka/meta.yml
@@ -10,7 +10,6 @@ tools:
       homepage: https://github.com/tseemann/prokka
       doi: "10.1093/bioinformatics/btu153"
       licence: ["GPL v2"]
-
 input:
   - meta:
       type: map
@@ -27,7 +26,6 @@ input:
   - prodigal_tf:
       type: file
       description: Training file to use for Prodigal (optional)
-
 output:
   - meta:
       type: map
@@ -86,6 +84,7 @@ output:
       type: file
       description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)
       pattern: "*.{tsv}"
-
 authors:
   - "@rpetit3"
+maintainers:
+  - "@rpetit3"
diff --git a/modules/nf-core/prokka/tests/main.nf.test b/modules/nf-core/prokka/tests/main.nf.test
new file mode 100644
index 00000000..3b59ef3a
--- /dev/null
+++ b/modules/nf-core/prokka/tests/main.nf.test
@@ -0,0 +1,46 @@
+nextflow_process {
+
+    name "Test Process PROKKA"
+    script "../main.nf"
+    process "PROKKA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "prokka"
+
+    test("Prokka - sarscov2 - genome.fasta") {
+
+        when {
+            process {
+                """
+                input[0] =  Channel.fromList([
+                        tuple([ id:'test', single_end:false ], // meta map
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true))
+                    ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.gff).match("gff") },
+                { assert snapshot(process.out.fna).match("fna") },
+                { assert snapshot(process.out.faa).match("faa") },
+                { assert snapshot(process.out.ffn).match("ffn") },
+                { assert snapshot(process.out.fsa).match("fsa") },
+                { assert snapshot(process.out.tbl).match("tbl") },
+                { assert snapshot(process.out.err).match("err") },
+                { assert snapshot(process.out.txt).match("txt") },
+                { assert snapshot(process.out.tsv).match("tsv") },
+                { assert path(process.out.gbk.get(0).get(1)).exists() },
+                { assert path(process.out.log.get(0).get(1)).exists() },
+                { assert path(process.out.sqn.get(0).get(1)).exists() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/prokka/tests/main.nf.test.snap b/modules/nf-core/prokka/tests/main.nf.test.snap
new file mode 100644
index 00000000..859e8df8
--- /dev/null
+++ b/modules/nf-core/prokka/tests/main.nf.test.snap
@@ -0,0 +1,128 @@
+{
+    "txt": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.txt:md5,b40e485ffc8eaf1feacf8d79d9751a33"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.84139118"
+    },
+    "err": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.err:md5,b3daedc646fddd422824e2b3e5e9229d"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.837204155"
+    },
+    "fsa": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fsa:md5,71bbefcb7f12046bcd3263f58cfd5404"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.803513721"
+    },
+    "gff": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.gff:md5,5dbfb8fcf2db020564c16045976a0933"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.710100529"
+    },
+    "tsv": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.tsv:md5,da7c720c3018c5081d6a70b517b7d450"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.846026731"
+    },
+    "faa": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.faa:md5,a4ceda83262b3c222a6b1f508fb9e24b"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.722112433"
+    },
+    "fna": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fna:md5,787307f29a263e5657cc276ebbf7e2b3"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.717325796"
+    },
+    "ffn": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.ffn:md5,80f474b5367b7ea5ed23791935f65e34"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.727149899"
+    },
+    "tbl": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.tbl:md5,d8f816a066ced94b62d9618b13fb8add"
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-14T15:19:54.831206944"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/prokka/tests/tags.yml b/modules/nf-core/prokka/tests/tags.yml
new file mode 100644
index 00000000..a2dc7bdc
--- /dev/null
+++ b/modules/nf-core/prokka/tests/tags.yml
@@ -0,0 +1,2 @@
+prokka:
+  - "modules/nf-core/prokka/**"
diff --git a/nextflow.config b/nextflow.config
index 774e2ad2..2c8b440a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -293,22 +293,16 @@ profiles {
         executor.cpus           = 4
         executor.memory         = 8.GB
     }
-    test                      { includeConfig 'conf/test.config'                      }
-    test_full                 { includeConfig 'conf/test_full.config'                 }
-    test_host_rm              { includeConfig 'conf/test_host_rm.config'              }
-    test_hybrid               { includeConfig 'conf/test_hybrid.config'               }
-    test_hybrid_host_rm       { includeConfig 'conf/test_hybrid_host_rm.config'       }
-    test_busco_auto           { includeConfig 'conf/test_busco_auto.config'           }
-    test_ancient_dna          { includeConfig 'conf/test_ancient_dna.config'          }
-    test_adapterremoval       { includeConfig 'conf/test_adapterremoval.config'       }
-    test_binning_entry        { includeConfig 'conf/test_binning_entry.config'        }
-    test_binrefinement        { includeConfig 'conf/test_binrefinement.config'        }
-    test_no_clipping          { includeConfig 'conf/test_no_clipping.config'          }
-    test_bbnorm               { includeConfig 'conf/test_bbnorm.config'               }
-    test_nothing              { includeConfig 'conf/test_nothing.config'              }
-    test_virus_identification { includeConfig 'conf/test_virus_identification.config' }
-    test_single_end           { includeConfig 'conf/test_single_end.config'           }
-    test_concoct              { includeConfig 'conf/test_concoct.config'              }
+    test                       { includeConfig 'conf/test.config'                       }
+    test_full                  { includeConfig 'conf/test_full.config'                  }
+    test_single_end            { includeConfig 'conf/test_single_end.config'            }
+    test_alternatives          { includeConfig 'conf/test_alternatives.config'          }
+    test_preassembly_binrefine { includeConfig 'conf/test_preassembly_binrefine.config' }
+    test_hybrid_host_rm        { includeConfig 'conf/test_hybrid_host_rm.config'        }
+    test_nothing               { includeConfig 'conf/test_nothing.config'               }
+    test_extras                { includeConfig 'conf/test_extras.config'                }
+    test_bigdb                 { includeConfig 'conf/test_bigdb.config'                 }
+    test_busco_auto            { includeConfig 'conf/test_busco_auto.config'            }
 }
 
 // Load nf-core custom profiles from different Institutions