diff --git a/.editorconfig b/.editorconfig
index dd9ffa53..72dda289 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index 364dd9b5..9d44ed38 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/circ
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/circrna _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/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 7b6bd16d..8f7ea0eb 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/circrna'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
@@ -33,7 +33,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 9590dcae..cbea731e 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/circrna'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dec281c1..69b4d2d9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -29,10 +29,10 @@ jobs:
 
     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
         with:
           version: "${{ matrix.NXF_VER }}"
 
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 08622fd5..2d20d644 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 505d843c..765c84e8 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
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: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
index b706875f..40acc23f 100644
--- a/.github/workflows/linting_comment.yml
+++ b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index d468aeaa..03ecfcf7 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
diff --git a/.nf-core.yml b/.nf-core.yml
index 3805dc81..e0b85a77 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -1 +1,2 @@
 repository_type: pipeline
+nf_core_version: "2.14.1"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index af57081f..4dc0f1dc 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
diff --git a/README.md b/README.md
index 5d61b9af..fe77e560 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/circrna)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/circrna)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circrna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circrna)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
diff --git a/conf/base.config b/conf/base.config
index c6e21d9c..35f36a91 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -57,17 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
-    withName:HISAT2_ALIGN {
-        // Workaround: This step sometimes failes irreproduceably
-        errorStrategy = 'retry'
-        maxRetries    = 2
-    }
-    withName:CIRIQUANT {
-        // Workaround: This step sometimes failes irreproduceably
-        errorStrategy = 'retry'
-        maxRetries    = 2
-    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 2e0a6320..1d82c383 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -18,14 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -357,16 +349,6 @@ if (!params.skip_trimming) {
         ]
     }
 
-    withName: CIRIQUANT_YML {
-        ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') }
-        publishDir = [
-            path: { "${params.outdir}/references/ciriquant" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
     withName: CIRIQUANT {
         ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') }
         publishDir = [
@@ -388,59 +370,6 @@ if (!params.skip_trimming) {
         ]
     }
 
-    withName: DCC_1ST_PASS {
-        ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') }
-        ext.args = [ "",
-            "--chimOutType Junctions WithinBAM",
-            "--outSAMunmapped Within",
-            "--outFilterType BySJout",
-            "--outReadsUnmapped None",
-            "--readFilesCommand zcat",
-            "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
-            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
-            "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
-            "--chimSegmentMin ${params.chimSegmentMin}"
-        ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/1st_pass" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_intermediates
-        ]
-    }
-
-    withName: DCC_SJDB {
-        ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') }
-        publishDir = [
-            path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/sjdb" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_intermediates
-        ]
-    }
-
-    withName: DCC_2ND_PASS {
-        ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') }
-        ext.args = [ "",
-            "--chimOutType Junctions WithinBAM",
-            "--outSAMunmapped Within",
-            "--outFilterType BySJout",
-            "--outReadsUnmapped None",
-            "--readFilesCommand zcat",
-            "--sjdbFileChrStartEnd dataset.SJ.out.tab",
-            "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}",
-            "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}",
-            "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}",
-            "--chimSegmentMin ${params.chimSegmentMin}"
-        ].join(' ').trim()
-        publishDir = [
-            path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/2nd_pass" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_intermediates
-        ]
-    }
-
     withName: DCC_MATE1_1ST_PASS {
         ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') }
         ext.prefix = { "${meta.id}_mate1" }
@@ -667,25 +596,11 @@ if (!params.skip_trimming) {
         ext.when = { params.module.split(',').contains('circrna_discovery') }
     }
 
-    withName: COUNTS_TO_BED {
-        ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'"
-        ext.suffix = "bed"
-    }
-
-    withName: UNIQUE_REGIONS {
-        ext.args = "-k 1,1 -k2,2n -k3,3n -u"
-        ext.suffix = "unique.bed"
-    }
-
     withName: COMBINE_TRANSCRIPTOME_GTFS {
         ext.args = "-k 1,1 -k3,3n -k4,4n"
         ext.suffix = "gtf"
     }
 
-    withName: CIRCULAR_TRANSCRIPTOME {
-        ext.args = "-nameOnly"
-    }
-
     withName: MARK_CIRCULAR {
         // GAWK process that marks FASTA headers.
         // Leaves headers starting with "ENS" and non-header lines as is.
diff --git a/docs/usage.md b/docs/usage.md
index 28e1fd7e..5c6337d5 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -327,6 +327,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - Pulls software from Docker Hub: [`nfcore/circrna`](https://hub.docker.com/r/nfcore/circrna/)
 - `apptainer`
   - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
+- `wave`
+  - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
diff --git a/modules.json b/modules.json
index 3cd8115e..acc410f5 100644
--- a/modules.json
+++ b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "bedtools/getfasta": {
                         "branch": "master",
-                        "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
+                        "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299",
                         "installed_by": ["modules"]
                     },
                     "bedtools/intersect": {
@@ -87,12 +87,12 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
+                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f",
+                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
                         "installed_by": ["modules"]
                     },
                     "gnu/sort": {
@@ -216,7 +216,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf
index 50549c7d..b316117d 100644
--- a/modules/nf-core/bedtools/getfasta/main.nf
+++ b/modules/nf-core/bedtools/getfasta/main.nf
@@ -1,5 +1,5 @@
 process BEDTOOLS_GETFASTA {
-    tag "$bed"
+    tag "$meta.id"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
@@ -8,19 +8,20 @@ process BEDTOOLS_GETFASTA {
         'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }"
 
     input:
-    path bed
+    tuple val(meta), path(bed)
     path fasta
 
     output:
-    path "*.fa"         , emit: fasta
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.fa"), emit: fasta
+    path "versions.yml"          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${bed.baseName}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$fasta" == "${prefix}.fa") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     bedtools \\
         getfasta \\
@@ -34,4 +35,16 @@ process BEDTOOLS_GETFASTA {
         bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$fasta" == "${prefix}.fa") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    touch ${prefix}.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bedtools/getfasta/meta.yml b/modules/nf-core/bedtools/getfasta/meta.yml
index 25fb19a1..41917fe3 100644
--- a/modules/nf-core/bedtools/getfasta/meta.yml
+++ b/modules/nf-core/bedtools/getfasta/meta.yml
@@ -8,9 +8,14 @@ tools:
   - bedtools:
       description: |
         A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
-      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - bed:
       type: file
       description: Bed feature file
@@ -20,6 +25,11 @@ input:
       description: Input fasta file
       pattern: "*.{fa,fasta}"
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Output fasta file with extracted sequences
diff --git a/modules/nf-core/bedtools/getfasta/tests/main.nf.test b/modules/nf-core/bedtools/getfasta/tests/main.nf.test
new file mode 100644
index 00000000..4da7552c
--- /dev/null
+++ b/modules/nf-core/bedtools/getfasta/tests/main.nf.test
@@ -0,0 +1,62 @@
+nextflow_process {
+
+    name "Test Process BEDTOOLS_GETFASTA"
+    script "../main.nf"
+    process "BEDTOOLS_GETFASTA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/getfasta"
+
+    test("sarscov2 - bed - fasta") {
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:false],
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+                    ]
+                
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bed - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:false],
+                    file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
+                    ]
+                
+                input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap b/modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap
new file mode 100644
index 00000000..69bf33f7
--- /dev/null
+++ b/modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "sarscov2 - bed - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa:md5,41c3a45a57a16c04f828d8f8bb52df70"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa:md5,41c3a45a57a16c04f828d8f8bb52df70"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T14:16:19.383758985"
+    },
+    "sarscov2 - bed - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-03T14:16:47.47010536"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/getfasta/tests/tags.yml b/modules/nf-core/bedtools/getfasta/tests/tags.yml
new file mode 100644
index 00000000..42ec3026
--- /dev/null
+++ b/modules/nf-core/bedtools/getfasta/tests/tags.yml
@@ -0,0 +1,2 @@
+bedtools/getfasta:
+  - "modules/nf-core/bedtools/getfasta/**"
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9e19a74c..d79f1c86 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -25,6 +25,11 @@ process FASTQC {
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
     def rename_to = old_new_pairs*.join(' ').join(' ')
     def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+
+    def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB')
+    // FastQC memory value allowed range (100 - 10000)
+    def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb)
+
     """
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
@@ -33,6 +38,7 @@ process FASTQC {
     fastqc \\
         $args \\
         --threads $task.cpus \\
+        --memory $fastqc_memory \\
         $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml
new file mode 100644
index 00000000..34513c7f
--- /dev/null
+++ b/modules/nf-core/gawk/environment.yml
@@ -0,0 +1,7 @@
+name: gawk
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - anaconda::gawk=5.1.0
diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
index f856a1f8..578b448c 100644
--- a/modules/nf-core/gawk/main.nf
+++ b/modules/nf-core/gawk/main.nf
@@ -41,10 +41,11 @@ process GAWK {
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
-    suffix = task.ext.suffix ?: "${input.getExtension}"
+    suffix = task.ext.suffix ?: "${input.getExtension()}"
+    def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch"
 
     """
-    touch ${prefix}.${suffix}
+    ${create_cmd} ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test
new file mode 100644
index 00000000..fce82ca9
--- /dev/null
+++ b/modules/nf-core/gawk/tests/main.nf.test
@@ -0,0 +1,56 @@
+nextflow_process {
+
+    name "Test Process GAWK"
+    script "../main.nf"
+    process "GAWK"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gawk"
+
+    test("convert fasta to bed") {
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("convert fasta to bed with program file") {
+        config "./nextflow_with_program_file.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[1] = Channel.of('BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}').collectFile(name:"program.txt")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap
new file mode 100644
index 00000000..ce207478
--- /dev/null
+++ b/modules/nf-core/gawk/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "convert fasta to bed with program file": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-04-05T11:00:28.097563"
+    },
+    "convert fasta to bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.02.0"
+        },
+        "timestamp": "2024-04-05T10:28:15.625869"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config
new file mode 100644
index 00000000..6e5d43a3
--- /dev/null
+++ b/modules/nf-core/gawk/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: GAWK {
+        ext.suffix = "bed"
+        ext.args2 = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\''
+    }
+}
diff --git a/modules/nf-core/gawk/tests/nextflow_with_program_file.config b/modules/nf-core/gawk/tests/nextflow_with_program_file.config
new file mode 100644
index 00000000..693ad419
--- /dev/null
+++ b/modules/nf-core/gawk/tests/nextflow_with_program_file.config
@@ -0,0 +1,5 @@
+process {
+    withName: GAWK {
+        ext.suffix = "bed"
+    }
+}
diff --git a/modules/nf-core/gawk/tests/tags.yml b/modules/nf-core/gawk/tests/tags.yml
new file mode 100644
index 00000000..72e4531d
--- /dev/null
+++ b/modules/nf-core/gawk/tests/tags.yml
@@ -0,0 +1,2 @@
+gawk:
+  - "modules/nf-core/gawk/**"
diff --git a/nextflow.config b/nextflow.config
index 1c8eaf0b..aab0c0f9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -122,104 +122,110 @@ try {
 }
 
 // Load nf-core/circrna custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/circrna.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config")
-// }
+try {
+    includeConfig "${params.custom_config_base}/pipeline/circrna.config"
+} catch (Exception e) {
+    System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config")
+}
 profiles {
     debug {
-        dumpHashes             = true
-        process.beforeScript   = 'echo $HOSTNAME'
-        cleanup                = false
+        dumpHashes              = true
+        process.beforeScript    = 'echo $HOSTNAME'
+        cleanup                 = false
         nextflow.enable.configProcessNamesValidation = true
     }
     conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        channels               = ['conda-forge', 'bioconda', 'defaults']
-        apptainer.enabled      = false
+        conda.enabled           = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        apptainer.enabled       = false
     }
     mamba {
-        conda.enabled          = true
-        conda.useMamba         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        conda.enabled           = true
+        conda.useMamba          = true
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     docker {
-        docker.enabled         = true
-        conda.enabled          = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-        docker.runOptions      = '-u $(id -u):$(id -g)'
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions      = '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        conda.enabled          = false
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     podman {
-        podman.enabled         = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        podman.enabled          = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     shifter {
-        shifter.enabled        = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        shifter.enabled         = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     charliecloud {
-        charliecloud.enabled   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
+        charliecloud.enabled    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        apptainer.enabled       = false
     }
     apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
         apptainer.runOptions   = '--no-mount tmp --writable-tmpfs'
     }
+    wave {
+        apptainer.ociAutoPull   = true
+        singularity.ociAutoPull = true
+        wave.enabled            = true
+        wave.freeze             = true
+        wave.strategy           = 'conda,container'
+    }
     gitpod {
-        executor.name          = 'local'
-        executor.cpus          = 4
-        executor.memory        = 8.GB
+        executor.name           = 'local'
+        executor.cpus           = 4
+        executor.memory         = 8.GB
     }
     test          { includeConfig 'conf/test.config'          }
     test_igenomes { includeConfig 'conf/test_igenomes.config' }
diff --git a/pyproject.toml b/pyproject.toml
deleted file mode 100644
index 56110621..00000000
--- a/pyproject.toml
+++ /dev/null
@@ -1,15 +0,0 @@
-# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
-# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
-[tool.ruff]
-line-length = 120
-target-version = "py38"
-cache-dir = "~/.cache/ruff"
-
-[tool.ruff.lint]
-select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
-
-[tool.ruff.lint.isort]
-known-first-party = ["nf_core"]
-
-[tool.ruff.lint.per-file-ignores]
-"__init__.py" = ["E402", "F401"]
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index 6c2c0b4b..9d382295 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -53,7 +53,8 @@ workflow PREPARE_GENOME {
                                     HISAT2_EXTRACTSPLICESITES.out.versions,
                                     HISAT2_BUILD.out.versions,
                                     SEGEMEHL_INDEX.out.versions,
-                                    STAR_GENOMEGENERATE.out.versions)
+                                    STAR_GENOMEGENERATE.out.versions,
+                                    SAMTOOLS_FAIDX.out.versions)
 
     emit:
     faidx        = SAMTOOLS_FAIDX.out.fai
diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf
index 67ea1f60..15c32930 100644
--- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf
@@ -140,6 +140,10 @@ workflow PIPELINE_COMPLETION {
             imNotification(summary_params, hook_url)
         }
     }
+
+    workflow.onError {
+        log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting"
+    }
 }
 
 /*
@@ -241,8 +245,16 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["manifest_map"] = workflow.manifest.toMap()
 
     // Pipeline DOI
-    meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
-    meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
+    if (meta.manifest_map.doi) {
+        // 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
+        def temp_doi_ref = ""
+        String[] manifest_doi = meta.manifest_map.doi.tokenize(",")
+        for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: <a href=\'https://doi.org/${doi_ref.replace("https://doi.org/", "").replace(" ", "")}\'>${doi_ref.replace("https://doi.org/", "").replace(" ", "")}</a>), "
+        meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2)
+    } else meta["doi_text"] = ""
+    meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
     meta["tool_citations"] = ""
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index a8b55d6f..14558c39 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" +