diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 1161630..e082f69 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -9,9 +9,8 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-:::info
-If you need help using or modifying nf-core/reportho then the best place to ask is on the nf-core Slack [#reportho](https://nfcore.slack.com/channels/reportho) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/reportho then the best place to ask is on the nf-core Slack [#reportho](https://nfcore.slack.com/channels/reportho) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
-receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index e4d2a64..acc0149 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/repo
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/reportho/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/reportho _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 748b431..073e187 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -35,7 +35,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 3df0161..324a961 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,4 +1,4 @@
 {
     "editor.defaultFormatter": "esbenp.prettier-vscode",
-    "editor.formatOnSave": true,
+    "editor.formatOnSave": true
 }
diff --git a/conf/modules.config b/conf/modules.config
index a81954b..f7989d5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -46,7 +46,7 @@ process {
         ]
     }
 
-    withName: 'FETCH_INSPECTOR_GROUP_LOCAL|FETCH_INSPECTOR_GROUP_ONLINE' {
+    withName: 'FETCH_INSPECTOR_GROUP_ONLINE' {
         publishDir = [
             path: { "${params.outdir}/orthologs/orthoinspector" },
             mode: params.publish_dir_mode,
diff --git a/conf/test.config b/conf/test.config
index fc9ded3..2a67104 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -29,3 +29,4 @@ params {
     skip_iqtree      = true
     fastme_bootstrap = 0
 }
+
diff --git a/docs/images/nf-core-reportho_logo_light.png b/docs/images/nf-core-reportho_logo_light.png
index 2ccb82d..f02910f 100644
Binary files a/docs/images/nf-core-reportho_logo_light.png and b/docs/images/nf-core-reportho_logo_light.png differ
diff --git a/modules.json b/modules.json
index 1e87009..251ab94 100644
--- a/modules.json
+++ b/modules.json
@@ -56,7 +56,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/local/convert_fasta.nf b/modules/local/convert_fasta.nf
index 7b32950..434e047 100644
--- a/modules/local/convert_fasta.nf
+++ b/modules/local/convert_fasta.nf
@@ -28,4 +28,16 @@ process CONVERT_FASTA {
         Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fa
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/convert_phylip.nf b/modules/local/convert_phylip.nf
index 11dab37..a574b65 100644
--- a/modules/local/convert_phylip.nf
+++ b/modules/local/convert_phylip.nf
@@ -28,4 +28,16 @@ process CONVERT_PHYLIP {
         Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phy
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Biopython: \$(pip show biopython | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/create_tcoffeetemplate.nf b/modules/local/create_tcoffeetemplate.nf
index 071c3bf..0b8b7d3 100644
--- a/modules/local/create_tcoffeetemplate.nf
+++ b/modules/local/create_tcoffeetemplate.nf
@@ -20,7 +20,10 @@ process CREATE_TCOFFEETEMPLATE {
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
     # Prep templates
-    for structure in \$(ls *.pdb); do id=`echo \$structure| awk  {'gsub(".pdb", "", \$0); print'}`; echo -e ">"\$id "_P_" "\${id}" >>${prefix}_template.txt ; done
+    for structure in \$(ls *.pdb); do
+        id=`echo \$structure | awk  {'gsub(".pdb", "", \$0); print'}`;
+        echo -e ">"\$id "_P_" "\${id}" >> ${prefix}_template.txt;
+    done
     """
 
     stub:
diff --git a/modules/local/dump_params.nf b/modules/local/dump_params.nf
index f354fe2..323189b 100644
--- a/modules/local/dump_params.nf
+++ b/modules/local/dump_params.nf
@@ -8,6 +8,13 @@ process DUMP_PARAMS {
 
     input:
     tuple val(meta), path(exact)
+    val uniprot_query
+    val use_structures
+    val use_centroid
+    val min_score
+    val skip_downstream
+    val use_iqtree
+    val use_fastme
 
     output:
     tuple val(meta), path("params.yml"), emit: params
@@ -19,14 +26,19 @@ process DUMP_PARAMS {
     """
     cat <<- END_PARAMS > params.yml
     id: ${meta.id}
-    uniprot_query: ${params.uniprot_query}
+    uniprot_query: ${uniprot_query}
     exact_match: \$(cat $exact)
-    use_structures: ${params.use_structures}
-    use_centroid: ${params.use_centroid}
-    min_score: ${params.min_score}
-    skip_downstream: ${params.skip_downstream}
-    use_iqtree: ${params.use_iqtree}
-    use_fastme: ${params.use_fastme}
+    use_structures: ${use_structures}
+    use_centroid: ${use_centroid}
+    min_score: ${min_score}
+    skip_downstream: ${skip_downstream}
+    use_iqtree: ${use_iqtree}
+    use_fastme: ${use_fastme}
     END_PARAMS
     """
+
+    stub:
+    """
+    touch params.yml
+    """
 }
diff --git a/modules/local/fetch_afdb_structures.nf b/modules/local/fetch_afdb_structures.nf
index d560887..92ceae5 100644
--- a/modules/local/fetch_afdb_structures.nf
+++ b/modules/local/fetch_afdb_structures.nf
@@ -31,4 +31,16 @@ process FETCH_AFDB_STRUCTURES {
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phy
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}"
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_eggnog_group_local.nf b/modules/local/fetch_eggnog_group_local.nf
index 32df3da..c1786f8 100644
--- a/modules/local/fetch_eggnog_group_local.nf
+++ b/modules/local/fetch_eggnog_group_local.nf
@@ -2,6 +2,11 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -33,4 +38,15 @@ process FETCH_EGGNOG_GROUP_LOCAL {
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_eggnog_group.txt
+    touch ${prefix}_eggnog_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_inspector_group_online.nf b/modules/local/fetch_inspector_group_online.nf
index aaff6cb..a0f51d4 100644
--- a/modules/local/fetch_inspector_group_online.nf
+++ b/modules/local/fetch_inspector_group_online.nf
@@ -32,4 +32,17 @@ process FETCH_INSPECTOR_GROUP_ONLINE {
         OrthoInspector Database: $inspector_version
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_inspector_group.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+        OrthoInspector Database: $inspector_version
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_oma_group_local.nf b/modules/local/fetch_oma_group_local.nf
index db08c55..07a813e 100644
--- a/modules/local/fetch_oma_group_local.nf
+++ b/modules/local/fetch_oma_group_local.nf
@@ -2,6 +2,11 @@ process FETCH_OMA_GROUP_LOCAL {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -36,4 +41,14 @@ process FETCH_OMA_GROUP_LOCAL {
     END_VERSIONS
     """
 
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_oma_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_oma_group_online.nf b/modules/local/fetch_oma_group_online.nf
index 7335b98..470612b 100644
--- a/modules/local/fetch_oma_group_online.nf
+++ b/modules/local/fetch_oma_group_online.nf
@@ -33,4 +33,17 @@ process FETCH_OMA_GROUP_ONLINE {
     \$(get_oma_version.py)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_oma_group.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    \$(get_oma_version.py)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_panther_group_local.nf b/modules/local/fetch_panther_group_local.nf
index aa178dd..60d4979 100644
--- a/modules/local/fetch_panther_group_local.nf
+++ b/modules/local/fetch_panther_group_local.nf
@@ -7,6 +7,11 @@ process FETCH_PANTHER_GROUP_LOCAL {
         'https://depot.galaxyproject.org/singularity/python:3.10' :
         'biocontainers/python:3.10' }"
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     input:
     tuple val(meta), path(uniprot_id), path(taxid), path(exact)
     path panther_db
@@ -30,4 +35,15 @@ process FETCH_PANTHER_GROUP_LOCAL {
         Python: \$(python --version | cut -f2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_panther_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_panther_group_online.nf b/modules/local/fetch_panther_group_online.nf
index 525746b..7df1363 100644
--- a/modules/local/fetch_panther_group_online.nf
+++ b/modules/local/fetch_panther_group_online.nf
@@ -32,4 +32,17 @@ process FETCH_PANTHER_GROUP_ONLINE {
         Panther Database: \$(cat panther_version.txt)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_panther_group.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+        Panther Database: \$(cat panther_version.txt)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/fetch_sequences_online.nf b/modules/local/fetch_sequences_online.nf
index 5242abe..eec8581 100644
--- a/modules/local/fetch_sequences_online.nf
+++ b/modules/local/fetch_sequences_online.nf
@@ -33,4 +33,19 @@ process FETCH_SEQUENCES_ONLINE {
     \$(get_oma_version.py)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_orthologs.fa
+    touch ${prefix}_seq_hits.txt
+    touch ${prefix}_seq_misses.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    \$(get_oma_version.py)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/filter_fasta.nf b/modules/local/filter_fasta.nf
index ecfd20e..35d7181 100644
--- a/modules/local/filter_fasta.nf
+++ b/modules/local/filter_fasta.nf
@@ -2,6 +2,11 @@ process FILTER_FASTA {
     tag "$meta.id"
     label 'process_single'
 
+    conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
+        'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
+
     conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
@@ -27,4 +32,15 @@ process FILTER_FASTA {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_filtered.fa
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/filter_hits.nf b/modules/local/filter_hits.nf
index c99b67f..5f0d78d 100644
--- a/modules/local/filter_hits.nf
+++ b/modules/local/filter_hits.nf
@@ -32,4 +32,17 @@ process FILTER_HITS {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_minscore_000.txt
+    touch ${prefix}_centroid.txt
+    touch ${prefix}_filtered_hits.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -f2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/identify_seq_online.nf b/modules/local/identify_seq_online.nf
index e61bb0b..2ada143 100644
--- a/modules/local/identify_seq_online.nf
+++ b/modules/local/identify_seq_online.nf
@@ -29,4 +29,18 @@ process IDENTIFY_SEQ_ONLINE {
         Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_id.txt
+    touch ${prefix}_taxid.txt
+    touch ${prefix}_exact.txt
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Python Requests: \$(pip show requests | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/make_report.nf b/modules/local/make_report.nf
index 4d5aacd..cfcdd97 100644
--- a/modules/local/make_report.nf
+++ b/modules/local/make_report.nf
@@ -6,7 +6,6 @@ process MAKE_REPORT {
         'docker://itrujnara/orthologs-report:1.0.0' :
         'itrujnara/orthologs-report:1.0.0' }"
 
-
     input:
     tuple val(meta), path(id), path(taxid), path(exact), path(score_table), path(filtered_hits), path(support_plot), path(venn_plot), path(jaccard_plot), path(orthostats), path(seq_hits), path(seq_misses), path(str_hits), path(str_misses), path(alignment), path(iqtree), path(fastme), path(params_file)
 
@@ -59,4 +58,19 @@ process MAKE_REPORT {
         Python: \$(python --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}_dist
+    touch ${prefix}_dist/${prefix}_run.sh
+
+    cat <<- END_VERSIONS > versions.yml
+    ${task.process}:
+        Node: \$(node --version)
+        Yarn: \$(yarn --version)
+        React: \$(yarn view react version)
+        Python: \$(python --version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/make_score_table.nf b/modules/local/make_score_table.nf
index 6f86bff..bf5d23a 100644
--- a/modules/local/make_score_table.nf
+++ b/modules/local/make_score_table.nf
@@ -27,4 +27,15 @@ process MAKE_SCORE_TABLE {
         Python: \$(python3 --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_score_table.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python3 --version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/make_stats.nf b/modules/local/make_stats.nf
index f1e7b3d..5d29f49 100644
--- a/modules/local/make_stats.nf
+++ b/modules/local/make_stats.nf
@@ -27,4 +27,15 @@ process MAKE_STATS {
         Python: \$(python3 --version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_stats.yml
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python3 --version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/plot_orthologs.nf b/modules/local/plot_orthologs.nf
index a79ac89..e7f4b0e 100644
--- a/modules/local/plot_orthologs.nf
+++ b/modules/local/plot_orthologs.nf
@@ -25,7 +25,20 @@ process PLOT_ORTHOLOGS {
 
     cat <<- END_VERSIONS > versions.yml
     "${task.process}"
-        R: \$(R --version | head -n 1 | cut -d ' ' -f 3)
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_supports.png
+    touch ${prefix}_venn.png
+    touch ${prefix}_jaccard.png
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/local/plot_tree.nf b/modules/local/plot_tree.nf
index 238df56..f05177d 100644
--- a/modules/local/plot_tree.nf
+++ b/modules/local/plot_tree.nf
@@ -24,7 +24,18 @@ process PLOT_TREE {
 
     cat <<- END_VERSIONS > versions.yml
     "${task.process}":
-        R: \$(R --version | head -n 1 | cut -d ' ' -f 3)
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: meta.id
+    """
+    touch ${prefix}_${method}_tree.png
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/local/stats2csv.nf b/modules/local/stats2csv.nf
index 362ff42..8f2dc05 100644
--- a/modules/local/stats2csv.nf
+++ b/modules/local/stats2csv.nf
@@ -28,4 +28,16 @@ process STATS2CSV {
         PyYAML: \$(pip show pyyaml | grep Version | cut -d ' ' -f 2)
     END_VERSIONS
     """
+
+    stub:
+    prefix = task.ext.prefix ?: meta.id
+    """
+    touch ${prefix}_stats.csv
+
+    cat <<- END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        PyYAML: \$(pip show pyyaml | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
 }
diff --git a/out/pipeline_info/execution_trace_2024-02-29_10-26-50.txt b/out/pipeline_info/execution_trace_2024-02-29_10-26-50.txt
deleted file mode 100644
index 6b739ac..0000000
--- a/out/pipeline_info/execution_trace_2024-02-29_10-26-50.txt
+++ /dev/null
@@ -1 +0,0 @@
-task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
diff --git a/out/pipeline_info/params_2024-02-29_10-26-54.json b/out/pipeline_info/params_2024-02-29_10-26-54.json
deleted file mode 100644
index 3a5a755..0000000
--- a/out/pipeline_info/params_2024-02-29_10-26-54.json
+++ /dev/null
@@ -1,39 +0,0 @@
-{
-    "input": "samplesheet_id.csv",
-    "uniprot_query": true,
-    "merge_strategy": "union",
-    "inspector_version": "Eukaryota2019",
-    "use_structures": true,
-    "multiqc_config": null,
-    "multiqc_title": null,
-    "multiqc_logo": null,
-    "max_multiqc_email_size": "25.MB",
-    "multiqc_methods_description": null,
-    "outdir": "out",
-    "publish_dir_mode": "copy",
-    "email": null,
-    "email_on_fail": null,
-    "plaintext_email": false,
-    "monochrome_logs": false,
-    "hook_url": null,
-    "help": false,
-    "version": false,
-    "config_profile_name": null,
-    "config_profile_description": null,
-    "custom_config_version": "master",
-    "custom_config_base": "https://raw.githubusercontent.com/nf-core/configs/master",
-    "config_profile_contact": null,
-    "config_profile_url": null,
-    "max_memory": "128.GB",
-    "max_cpus": 16,
-    "max_time": "240.h",
-    "validationFailUnrecognisedParams": false,
-    "validation-fail-unrecognised-params": false,
-    "validationLenientMode": false,
-    "validation-lenient-mode": false,
-    "validationSchemaIgnoreParams": "genomes,igenomes_base",
-    "validation-schema-ignore-params": "genomes,igenomes_base",
-    "validationShowHiddenParams": false,
-    "validation-show-hidden-params": false,
-    "validate_params": true
-}
\ No newline at end of file
diff --git a/subworkflows/local/get_orthologs.nf b/subworkflows/local/get_orthologs.nf
index 4db3d00..86fb6c2 100644
--- a/subworkflows/local/get_orthologs.nf
+++ b/subworkflows/local/get_orthologs.nf
@@ -145,8 +145,8 @@ workflow GET_ORTHOLOGS {
         ch_versions
             .mix(FETCH_EGGNOG_GROUP_LOCAL.out.versions)
             .set { ch_versions }
-
-    } else { // online/local separation is used
+    }
+    else { // online/local separation is used
         // local only
         if (params.local_databases) {
             if (!params.skip_oma) {
diff --git a/subworkflows/local/report.nf b/subworkflows/local/report.nf
index a1ea745..47e061d 100644
--- a/subworkflows/local/report.nf
+++ b/subworkflows/local/report.nf
@@ -3,7 +3,15 @@ include { MAKE_REPORT    } from "../../modules/local/make_report"
 include { CONVERT_FASTA } from "../../modules/local/convert_fasta"
 
 workflow REPORT {
+
     take:
+    uniprot_query
+    use_structures
+    use_centroid
+    min_score
+    skip_downstream
+    use_iqtree
+    use_fastme
     ch_seqinfo
     ch_scoretable
     ch_filtered
@@ -43,7 +51,14 @@ workflow REPORT {
     }
 
     DUMP_PARAMS(
-        ch_seqinfo.map { [it[0], it[3]] }
+        ch_seqinfo.map { [it[0], it[3]] },
+        params.uniprot_query,
+        params.use_structures,
+        params.use_centroid,
+        params.min_score,
+        params.skip_downstream,
+        params.skip_iqtree,
+        params.skip_fastme
     )
 
     if(!params.skip_downstream) {
diff --git a/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf b/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf
index 3526ccc..be134bc 100644
--- a/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_reportho_pipeline/main.nf
@@ -72,10 +72,6 @@ workflow PIPELINE_INITIALISATION {
     UTILS_NFCORE_PIPELINE (
         nextflow_cli_args
     )
-    //
-    // Custom validation for pipeline parameters
-    //
-    validateInputParameters()
 
     //
     // Create channel from input file provided through params.input
@@ -135,12 +131,9 @@ workflow PIPELINE_COMPLETION {
     FUNCTIONS
 ========================================================================================
 */
+
+
 //
-// Check and validate pipeline parameters
-//
-def validateInputParameters() {
-    genomeExistsError()
-}//
 // Validate channels from input samplesheet
 //
 def validateInputSamplesheet(input) {
@@ -156,31 +149,8 @@ def validateInputSamplesheet(input) {
 
     return input
 }
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
-    }
-    return null
-}
 
 //
-// Exit pipeline if incorrect --genome key provided
-//
-def genomeExistsError() {
-    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-            "  Currently, the available genome keys are:\n" +
-            "  ${params.genomes.keySet().join(", ")}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        error(error_string)
-    }
-}//
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6..14558c3 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
     return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
         "* The pipeline\n" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
index 10f948e..1037232 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap
@@ -1,25 +1,41 @@
 {
     "Test Function checkProfileProvided": {
         "content": null,
-        "timestamp": "2024-02-09T15:43:55.145717"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:03.360873"
     },
     "Test Function checkConfigProvided": {
         "content": [
             true
         ],
-        "timestamp": "2024-01-19T11:34:13.548431224"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:02:59.729647"
     },
     "Test Function nfCoreLogo": {
         "content": [
             "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n                                        \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m        ___     __   __   __   ___     \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \u001b[0;33m}  {\u001b[0m\n\u001b[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \u001b[0;32m\\`-._,-`-,\u001b[0m\n                                        \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m  nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n"
         ],
-        "timestamp": "2024-01-19T11:34:38.840454873"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:10.562934"
     },
     "Test Function workflowCitation": {
         "content": [
             "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n  https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n  https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n  https://github.com/nextflow_workflow/blob/master/CITATIONS.md"
         ],
-        "timestamp": "2024-01-19T11:34:22.24352016"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:07.019761"
     },
     "Test Function without logColours": {
         "content": [
@@ -73,13 +89,21 @@
                 "biwhite": ""
             }
         ],
-        "timestamp": "2024-01-19T11:35:04.418416984"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:17.969323"
     },
     "Test Function dashedLine": {
         "content": [
             "-\u001b[2m----------------------------------------------------\u001b[0m-"
         ],
-        "timestamp": "2024-01-19T11:34:55.420000755"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:14.366181"
     },
     "Test Function with logColours": {
         "content": [
@@ -133,6 +157,10 @@
                 "biwhite": "\u001b[1;97m"
             }
         ],
-        "timestamp": "2024-01-19T11:35:13.436366565"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:21.714424"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
index d07ce54..859d103 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap
@@ -10,6 +10,10 @@
                 ]
             }
         ],
-        "timestamp": "2024-01-19T11:35:22.538940073"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-02-28T12:03:25.726491"
     }
 }
\ No newline at end of file
diff --git a/workflows/reportho.nf b/workflows/reportho.nf
index b5b26a1..88328b4 100644
--- a/workflows/reportho.nf
+++ b/workflows/reportho.nf
@@ -107,6 +107,13 @@ workflow REPORTHO {
 
     if(!params.skip_report) {
         REPORT (
+            params.uniprot_query,
+            params.use_structures,
+            params.use_centroid,
+            params.min_score,
+            params.skip_downstream,
+            params.skip_iqtree,
+            params.skip_fastme,
             GET_ORTHOLOGS.out.seqinfo,
             GET_ORTHOLOGS.out.score_table,
             GET_ORTHOLOGS.out.orthologs,