diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 4dde8d56..72c2b4ae 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/fetc
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/fetchngs/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/fetchngs _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 (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] 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 073e1876..1fcafe88 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875f..40acc23f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/CHANGELOG.md b/CHANGELOG.md
index dbfb81be..234bb84d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
+- [PR #319](https://github.com/nf-core/fetchngs/pull/319) - Update subworkflows and modules to be TES compliance.
+
+### :warning: Major enhancements
+
+- All the subworkflows and modules have been updated to newest main branch of `nf-core/modules`
+- Add support for tags
+- Updated `multiqc_mappings_config` to have different matching pattern for `config.yml` vs `versions.yml`
 
 ### Software dependencies
 
diff --git a/modules.json b/modules.json
index c6b234bb..b37bf4e5 100644
--- a/modules.json
+++ b/modules.json
@@ -7,23 +7,23 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
                         "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
+                        "git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     }
                 }
@@ -37,12 +37,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config/main.nf
index 8efe1caa..5d809e52 100644
--- a/modules/local/multiqc_mappings_config/main.nf
+++ b/modules/local/multiqc_mappings_config/main.nf
@@ -10,7 +10,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     path csv
 
     output:
-    path "*yml"        , emit: yml
+    path "*config.yml"        , emit: yml
     path "versions.yml", emit: versions
 
     script:
diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
index 44a1b008..cd4c3fbe 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/environment.yml
+++ b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
@@ -1,7 +1,5 @@
-name: custom_sratoolsncbisettings
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::sra-tools=3.0.8
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
index e9ea68dc..b8b95320 100644
--- a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
@@ -4,6 +4,10 @@ nextflow_process {
     script "../main.nf"
     process "CUSTOM_SRATOOLSNCBISETTINGS"
     config "modules/nf-core/custom/sratoolsncbisettings/tests/nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom"
+    tag "custom/sratoolsncbisettings"
 
     test("Should run without failures") {
 
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
new file mode 100644
index 00000000..fb4a08a7
--- /dev/null
+++ b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
@@ -0,0 +1,2 @@
+custom/sratoolsncbisettings:
+  - modules/nf-core/custom/sratoolsncbisettings/**
diff --git a/modules/nf-core/sratools/fasterqdump/environment.yml b/modules/nf-core/sratools/fasterqdump/environment.yml
index dd0faa56..970dfbc0 100644
--- a/modules/nf-core/sratools/fasterqdump/environment.yml
+++ b/modules/nf-core/sratools/fasterqdump/environment.yml
@@ -1,8 +1,6 @@
-name: sratools_fasterqdump
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::sra-tools=2.11.0
+  - bioconda::sra-tools=3.0.8
   - conda-forge::pigz=2.6
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
index e7cf157a..d5b65bab 100644
--- a/modules/nf-core/sratools/fasterqdump/main.nf
+++ b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -4,8 +4,8 @@ process SRATOOLS_FASTERQDUMP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' :
-        'quay.io/biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:6a9ff0e76ec016c3d0d27e0c0d362339f2d787e6-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' :
+        'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }"
 
     input:
     tuple val(meta), path(sra)
@@ -23,7 +23,10 @@ process SRATOOLS_FASTERQDUMP {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def outfile = meta.single_end ? "${prefix}.fastq" : prefix
+    def outfile = "${prefix}.fastq"
+    def exclude_third = meta.single_end ? '' : "mv $outfile $prefix || echo 'No third file'"
+    // Excludes the "${prefix}.fastq" file from output `reads` channel for paired end cases and
+    // avoids the '.' in the path bug: https://github.com/ncbi/sra-tools/issues/865
     def key_file = ''
     if (certificate.toString().endsWith('.jwt')) {
         key_file += " --perm ${certificate}"
@@ -40,6 +43,51 @@ process SRATOOLS_FASTERQDUMP {
         ${key_file} \\
         ${sra}
 
+    $exclude_third
+
+    pigz \\
+        $args2 \\
+        --no-name \\
+        --processes $task.cpus \\
+        *.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def outfile = "${prefix}.fastq"
+    def exclude_third = meta.single_end ? '' : "mv $outfile $prefix || echo 'No third file'"
+    // Excludes the "${prefix}.fastq" file from output `reads` channel for paired end cases and
+    // avoids the '.' in the path bug: https://github.com/ncbi/sra-tools/issues/865
+    def key_file = ''
+    if (certificate.toString().endsWith('.jwt')) {
+        key_file += " --perm ${certificate}"
+    } else if (certificate.toString().endsWith('.ngc')) {
+        key_file += " --ngc ${certificate}"
+    }
+    def touch_outfiles = meta.single_end ? "${prefix}.fastq" : "${prefix}_1.fastq ${prefix}_2.fastq"
+    """
+    touch $touch_outfiles
+
+    export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
+
+    echo \\
+    "fasterq-dump \\
+        $args \\
+        --threads $task.cpus \\
+        --outfile $outfile \\
+        ${key_file} \\
+        ${sra}"
+
+    $exclude_third
+
     pigz \\
         $args2 \\
         --no-name \\
diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml
index b5e0175a..6a2151a8 100644
--- a/modules/nf-core/sratools/fasterqdump/meta.yml
+++ b/modules/nf-core/sratools/fasterqdump/meta.yml
@@ -51,3 +51,4 @@ authors:
   - "@Midnighter"
 maintainers:
   - "@Midnighter"
+  - "@gallvp"
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
index 695394d4..6996cd18 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -1,10 +1,12 @@
 nextflow_process {
     name "Test Process SRATOOLS_FASTERQDUMP"
     script "../main.nf"
-    config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
-
-    tag "UNTAR"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+    tag "sratools"
+    tag "sratools/fasterqdump"
 
     test("Single-end") {
 
@@ -67,4 +69,54 @@ nextflow_process {
             )
         }
     }
+
+    test("Single-end-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_single_end', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Paired-end-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_paired_end', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
index ce0f9800..5d0c3e7c 100644
--- a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ],
                 "reads": [
                     [
@@ -24,15 +24,50 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-28T15:25:52.837288"
+        "timestamp": "2024-05-17T22:01:43.486256"
+    },
+    "Single-end-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T21:40:42.335786"
     },
     "Paired-end": {
         "content": [
@@ -50,7 +85,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ],
                 "reads": [
                     [
@@ -65,14 +100,55 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6ff2d50b15c3f0eb9c72cd13a4a20295"
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T22:09:55.6396"
+    },
+    "Paired-end-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_paired_end_2.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_paired_end_2.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-28T15:26:42.466223"
+        "timestamp": "2024-05-17T20:35:44.782058"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/nextflow.config b/modules/nf-core/sratools/fasterqdump/tests/nextflow.config
deleted file mode 100644
index 23e4100b..00000000
--- a/modules/nf-core/sratools/fasterqdump/tests/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: SRATOOLS_FASTERQDUMP {
-        ext.args = ''
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/sratools/fasterqdump/tests/tags.yml b/modules/nf-core/sratools/fasterqdump/tests/tags.yml
new file mode 100644
index 00000000..5d1ddcb3
--- /dev/null
+++ b/modules/nf-core/sratools/fasterqdump/tests/tags.yml
@@ -0,0 +1,2 @@
+sratools/fasterqdump:
+  - modules/nf-core/sratools/fasterqdump/**
diff --git a/modules/nf-core/sratools/prefetch/environment.yml b/modules/nf-core/sratools/prefetch/environment.yml
index 0abad336..6596bc7c 100644
--- a/modules/nf-core/sratools/prefetch/environment.yml
+++ b/modules/nf-core/sratools/prefetch/environment.yml
@@ -1,8 +1,6 @@
-name: sratools_prefetch
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::sra-tools=3.1.0
   - conda-forge::curl=8.5.0
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
index 170f1753..74838d53 100644
--- a/modules/nf-core/sratools/prefetch/main.nf
+++ b/modules/nf-core/sratools/prefetch/main.nf
@@ -13,7 +13,7 @@ process SRATOOLS_PREFETCH {
     path certificate
 
     output:
-    tuple val(meta), path(id), emit: sra
+    tuple val(meta), path(id, type: 'dir'), emit: sra
     path 'versions.yml'      , emit: versions
 
     when:
@@ -32,4 +32,16 @@ process SRATOOLS_PREFETCH {
     }
 
     template 'retry_with_backoff.sh'
+
+    stub:
+    """
+    mkdir $id
+    touch $id/${id}.sra
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+        curl: \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml
index ff54229f..7ed42d49 100644
--- a/modules/nf-core/sratools/prefetch/meta.yml
+++ b/modules/nf-core/sratools/prefetch/meta.yml
@@ -54,3 +54,4 @@ authors:
   - "@Midnighter"
 maintainers:
   - "@Midnighter"
+  - "@gallvp"
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
index f59de7cb..92034d40 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -46,4 +46,26 @@ nextflow_process {
             )
         }
     }
+
+    test("sratools/prefetch/stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
index 67795ebb..a1f82f45 100644
--- a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
+++ b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
@@ -1,4 +1,43 @@
 {
+    "sratools/prefetch/stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "DRR000774.sra:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
+                ],
+                "sra": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "DRR000774.sra:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T20:07:31.627115"
+    },
     "sratools/prefetch with sralite": {
         "content": [
             {
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml
index 0c9cbb10..c7794856 100644
--- a/modules/nf-core/untar/environment.yml
+++ b/modules/nf-core/untar/environment.yml
@@ -1,11 +1,7 @@
-name: untar
-
 channels:
   - conda-forge
   - bioconda
-  - defaults
-
 dependencies:
   - conda-forge::grep=3.11
-  - conda-forge::sed=4.7
+  - conda-forge::sed=4.8
   - conda-forge::tar=1.34
diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf
index 8a75bb95..9bd8f554 100644
--- a/modules/nf-core/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -4,8 +4,8 @@ process UNTAR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'nf-core/ubuntu:20.04' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:22.04' :
+        'nf-core/ubuntu:22.04' }"
 
     input:
     tuple val(meta), path(archive)
@@ -52,8 +52,29 @@ process UNTAR {
     stub:
     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, ""))
     """
-    mkdir $prefix
-    touch ${prefix}/file.txt
+    mkdir ${prefix}
+    ## Dry-run untaring the archive to get the files and place all in prefix
+    if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+        for i in `tar -tf ${archive}`;
+        do
+            if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]];
+            then
+                touch \${i}
+            else
+                mkdir -p \${i}
+            fi
+        done
+    else
+        for i in `tar -tf ${archive}`;
+        do
+            if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]];
+            then
+                touch ${prefix}/\${i}
+            else
+                mkdir -p ${prefix}/\${i}
+            fi
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
index 98b769ad..c957517a 100644
--- a/modules/nf-core/untar/tests/main.nf.test
+++ b/modules/nf-core/untar/tests/main.nf.test
@@ -3,7 +3,10 @@ nextflow_process {
     name "Test Process UNTAR"
     script "../main.nf"
     process "UNTAR"
-    
+    tag "modules"
+    tag "modules_nfcore"
+    tag "untar"
+
     test("test_untar") {
 
         when {
@@ -17,10 +20,9 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.untar).match("test_untar") },
+                { assert snapshot(process.out).match() },
             )
         }
-
     }
 
     test("test_untar_onlyfiles") {
@@ -36,10 +38,48 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out.untar).match("test_untar_onlyfiles") },
+                { assert snapshot(process.out).match() },
             )
         }
+    }
+
+    test("test_untar - stub") {
+
+        options "-stub"
 
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
     }
 
+    test("test_untar_onlyfiles - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
index 64550292..ceb91b79 100644
--- a/modules/nf-core/untar/tests/main.nf.test.snap
+++ b/modules/nf-core/untar/tests/main.nf.test.snap
@@ -1,42 +1,158 @@
 {
     "test_untar_onlyfiles": {
         "content": [
-            [
-                [
+            {
+                "0": [
                     [
-                        
-                    ],
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T12:04:28.231047"
+    },
+    "test_untar_onlyfiles - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
                     [
-                        "hello.txt:md5,e59ff97941044f85df5297e1c302d260"
+                        [
+                            
+                        ],
+                        [
+                            "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-28T11:49:41.320643"
+        "timestamp": "2024-07-10T12:04:45.773103"
+    },
+    "test_untar - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-10T12:04:36.777441"
     },
     "test_untar": {
         "content": [
-            [
-                [
+            {
+                "0": [
                     [
-                        
-                    ],
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+                            "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+                            "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
+                ],
+                "untar": [
                     [
-                        "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
-                        "opts.k2d:md5,a033d00cf6759407010b21700938f543",
-                        "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                        [
+                            
+                        ],
+                        [
+                            "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9",
+                            "opts.k2d:md5,a033d00cf6759407010b21700938f543",
+                            "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c"
+                        ]
                     ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6063247258c56fd271d076bb04dd7536"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-02-28T11:49:33.795172"
+        "timestamp": "2024-07-10T12:04:19.377674"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
new file mode 100644
index 00000000..feb6f15c
--- /dev/null
+++ b/modules/nf-core/untar/tests/tags.yml
@@ -0,0 +1,2 @@
+untar:
+  - modules/nf-core/untar/**
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
index 0c0be2a4..1a34e0b8 100644
--- a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test.snap
@@ -40,8 +40,8 @@
         "content": [
             [
                 "versions.yml:md5,1a2218ff913fc33408bffccb081b5048",
-                "versions.yml:md5,2f3b3a13b36dabf13f09327613d5558d",
-                "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3"
+                "versions.yml:md5,53d6e983afde3a28add2ffc6b7eba4f3",
+                "versions.yml:md5,9c558ff624585a6eee82a19c8c0136db"
             ]
         ],
         "meta": {
@@ -52,7 +52,7 @@
     },
     "test_pe_reads_1_size": {
         "content": [
-            2013376
+            2011460
         ],
         "meta": {
             "nf-test": "0.8.4",
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28f..28e32b20 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
 // Subworkflow with functionality that may be useful for any Nextflow pipeline
 //
 
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
 // Generate version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
     def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
     def filename   = "params_${timestamp}.json"
     def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
-    def jsonStr    = JsonOutput.toJson(params)
-    temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+    def jsonStr    = groovy.json.JsonOutput.toJson(params)
+    temp_pf.text   = groovy.json.JsonOutput.prettyPrint(jsonStr)
 
-    FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+    nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
     temp_pf.delete()
 }
 
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
 // When running with -profile conda, warn if channels have not been set-up appropriately
 //
 def checkCondaChannels() {
-    Yaml parser = new Yaml()
+    def parser = new org.yaml.snakeyaml.Yaml()
     def channels = []
     try {
         def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
 
     // Check that all channels are present
     // This channel list is ordered by required channel priority.
-    def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+    def required_channels_in_order = ['conda-forge', 'bioconda']
     def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
     // Check that they are in the right order
     def channel_priority_violation = false
-    def n = required_channels_in_order.size()
-    for (int i = 0; i < n - 1; i++) {
-        channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+    required_channels_in_order.eachWithIndex { channel, index ->
+        if (index < required_channels_in_order.size() - 1) {
+            channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+        }
     }
 
     if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
index e49d617f..68718e4f 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test
@@ -4,7 +4,9 @@ nextflow_function {
     name "Test Functions"
     script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
-    tag "UTILS_NEXTFLOW_PIPELINE"
+    tag 'subworkflows'
+    tag 'utils_nextflow_pipeline'
+    tag 'subworkflows/utils_nextflow_pipeline'
 
     test("Test Function getWorkflowVersion") {
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
index 13782037..ca964ce8 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
@@ -4,6 +4,9 @@ nextflow_workflow {
     script "../main.nf"
     config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config"
     workflow "UTILS_NEXTFLOW_PIPELINE"
+    tag 'subworkflows'
+    tag 'utils_nextflow_pipeline'
+    tag 'subworkflows/utils_nextflow_pipeline'
 
     test("Should run no inputs") {
 
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926bf..a09572e5 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
     author          = """nf-core"""
     homePage        = 'https://127.0.0.1'
     description     = """Dummy pipeline"""
-    nextflowVersion  = '!>=23.04.0'
+    nextflowVersion = '!>=23.04.0'
     version         = '9.9.9'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
new file mode 100644
index 00000000..f8476112
--- /dev/null
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nextflow_pipeline:
+  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..cbd8495b 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
 // Subworkflow with utility functions specific to the nf-core pipeline template
 //
 
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
 /*
 ========================================================================================
     SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
 //  Warn if a -profile or Nextflow config has not been provided to run the pipeline
 //
 def checkConfigProvided() {
-    valid_config = true
+    def valid_config = true as Boolean
     if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
         log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
             "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -65,9 +62,17 @@ def checkProfileProvided(nextflow_cli_args) {
 // Citation string for pipeline
 //
 def workflowCitation() {
+    def temp_doi_ref = ""
+    def manifest_doi = workflow.manifest.doi.tokenize(",")
+    // Using a loop to handle multiple DOIs
+    // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
+    // Removing ` ` since the manifest.doi is a string and not a proper list
+    manifest_doi.each { doi_ref ->
+        temp_doi_ref += "  https://doi.org/${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" +
-        "  ${workflow.manifest.doi}\n\n" +
+        temp_doi_ref + "\n" +
         "* The nf-core framework\n" +
         "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
         "* Software dependencies\n" +
@@ -78,7 +83,7 @@ def workflowCitation() {
 // Generate workflow version string
 //
 def getWorkflowVersion() {
-    String version_string = ""
+    def version_string = "" as String
     if (workflow.manifest.version) {
         def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
         version_string += "${prefix_v}${workflow.manifest.version}"
@@ -96,8 +101,8 @@ def getWorkflowVersion() {
 // Get software versions for pipeline
 //
 def processVersionsFromYAML(yaml_file) {
-    Yaml yaml = new Yaml()
-    versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+    def yaml = new org.yaml.snakeyaml.Yaml()
+    def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
     return yaml.dumpAsMap(versions).trim()
 }
 
@@ -118,7 +123,7 @@ def workflowVersionToYAML() {
 def softwareVersionsToYAML(ch_versions) {
     return ch_versions
                 .unique()
-                .map { processVersionsFromYAML(it) }
+                .map { version -> processVersionsFromYAML(version) }
                 .unique()
                 .mix(Channel.of(workflowVersionToYAML()))
 }
@@ -128,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
 //
 def paramsSummaryMultiqc(summary_params) {
     def summary_section = ''
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().each { group ->
         def group_params = summary_params.get(group)  // This gets the parameters of that particular group
         if (group_params) {
             summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
             summary_section += "    <dl class=\"dl-horizontal\">\n"
-            for (param in group_params.keySet()) {
+            group_params.keySet().sort().each { param ->
                 summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
             }
             summary_section += "    </dl>\n"
         }
     }
 
-    String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+    def yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
     yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
     yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
     yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -155,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
 // nf-core logo
 //
 def nfCoreLogo(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     String.format(
         """\n
         ${dashedLine(monochrome_logs)}
@@ -174,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
 // Return dashed line
 //
 def dashedLine(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     return "-${colors.dim}----------------------------------------------------${colors.reset}-"
 }
 
@@ -182,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
 // ANSII colours used for terminal logging
 //
 def logColours(monochrome_logs=true) {
-    Map colorcodes = [:]
+    def colorcodes = [:] as Map
 
     // Reset / Meta
     colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
@@ -281,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     }
 
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
@@ -338,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     def sendmail_html          = sendmail_template.toString()
 
     // Send the HTML e-mail
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (email_address) {
         try {
-            if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+            if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
             // Try to send HTML e-mail using sendmail
             def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
             sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -358,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
     // Write summary e-mail HTML to a file
     def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
     output_hf.withWriter { w -> w << email_html }
-    FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+    nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
     output_hf.delete()
 
     // Write summary e-mail TXT to a file
     def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
     output_tf.withWriter { w -> w << email_txt }
-    FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+    nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
     output_tf.delete()
 }
 
@@ -372,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
 // Print pipeline summary on completion
 //
 def completionSummary(monochrome_logs=true) {
-    Map colors = logColours(monochrome_logs)
+    def colors = logColours(monochrome_logs) as Map
     if (workflow.success) {
         if (workflow.stats.ignoredCount == 0) {
             log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -389,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
 //
 def imNotification(summary_params, hook_url) {
     def summary = [:]
-    for (group in summary_params.keySet()) {
+    summary_params.keySet().sort().each { group ->
         summary << summary_params[group]
     }
 
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
new file mode 100644
index 00000000..ac8523c9
--- /dev/null
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/utils_nfcore_pipeline:
+  - subworkflows/nf-core/utils_nfcore_pipeline/**