From e88a4bfb7c5b9f174a1f0a7ad8484f7bc89526e4 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 20 Nov 2025 09:32:46 +0000
Subject: [PATCH 1/5] Template update for nf-core/tools version 3.5.1

---
 .github/workflows/awsfulltest.yml             |  2 +-
 .github/workflows/awstest.yml                 |  2 +-
 .github/workflows/download_pipeline.yml       |  2 +-
 .github/workflows/fix_linting.yml             |  2 +-
 .github/workflows/linting.yml                 |  6 +--
 .github/workflows/nf-test.yml                 |  4 +-
 .github/workflows/release-announcements.yml   |  9 ++---
 .../workflows/template-version-comment.yml    |  2 +-
 .nf-core.yml                                  |  2 +-
 .prettierignore                               |  2 +
 README.md                                     |  4 +-
 modules.json                                  |  4 +-
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 +-
 .../nf-core/multiqc/tests/main.nf.test.snap   | 24 ++++++------
 nextflow.config                               |  2 -
 ro-crate-metadata.json                        | 14 +++----
 .../utils_nfcore_rnaseq_pipeline/main.nf      |  6 +--
 .../nf-core/utils_nfcore_pipeline/main.nf     |  2 +-
 workflows/rnaseq.nf                           | 38 ++++++++++++++-----
 20 files changed, 74 insertions(+), 59 deletions(-)

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 1c047e39a..94b614f11 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.github/workflows/awsfulltest.yml
@@ -40,7 +40,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 1955894c9..0a85c67f8 100644
--- a/.github/workflows/awstest.yml
+++ b/.github/workflows/awstest.yml
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 6d94bcbf9..45884ff90 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -127,7 +127,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*
diff --git a/.github/workflows/fix_linting.yml b/.github/workflows/fix_linting.yml
index 781602a8d..0d99fdd5b 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@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 30e66026f..7a527a346 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -11,7 +11,7 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Set up Python 3.14
         uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -71,7 +71,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: linting-logs
           path: |
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index e20bf6d0c..c98d76ec7 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
@@ -85,7 +85,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
index e64cebd6a..431d3d445 100644
--- a/.github/workflows/release-announcements.yml
+++ b/.github/workflows/release-announcements.yml
@@ -15,10 +15,9 @@ jobs:
           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' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT
 
       - name: get description
-        id: get_topics
+        id: get_description
         run: |
-          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description' >> $GITHUB_OUTPUT
-
+          echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -27,9 +26,7 @@ jobs:
           # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
           message: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            ${{ steps.get_topics.outputs.description }}
-
+            ${{ steps.get_description.outputs.description }}
             Please see the changelog: ${{ github.event.release.html_url }}
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
diff --git a/.github/workflows/template-version-comment.yml b/.github/workflows/template-version-comment.yml
index c5988af90..e8560fc7c 100644
--- a/.github/workflows/template-version-comment.yml
+++ b/.github/workflows/template-version-comment.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5
+        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 
diff --git a/.nf-core.yml b/.nf-core.yml
index 6f6c71c2d..58adf2d17 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -10,7 +10,7 @@ lint:
   nextflow_config:
     - config_defaults:
         - params.ribo_database_manifest
-nf_core_version: 3.4.1
+nf_core_version: 3.5.1
 repository_type: pipeline
 template:
   author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n"
diff --git a/.prettierignore b/.prettierignore
index 2255e3e36..dd749d43d 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -12,3 +12,5 @@ testing*
 bin/
 .nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/
diff --git a/README.md b/README.md
index 2dab938a0..3543c6298 100644
--- a/README.md
+++ b/README.md
@@ -5,13 +5,13 @@
   </picture>
 </h1>
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/rnaseq)
+[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/rnaseq)
 [![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![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/)
diff --git a/modules.json b/modules.json
index 7ee9b05d6..b806a6ce2 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
                         "installed_by": ["modules"]
                     }
                 }
@@ -26,7 +26,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index dd513cbd1..d02016a00 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.31
+  - bioconda::multiqc=1.32
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 5288f5ccf..c1158fb08 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' :
-        'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
+        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 17881d15c..a88bafd67 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
+                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-09-08T20:57:36.139055243"
+        "timestamp": "2025-10-27T13:33:24.356715"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
+                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-09-08T20:59:15.142230631"
+        "timestamp": "2025-10-27T13:34:11.103619"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
+                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-09-08T20:58:29.629087066"
+        "timestamp": "2025-10-27T13:34:04.615233"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index e955da859..e40d71a2e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -170,8 +170,6 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
-// Set AWS client to anonymous when using the default igenomes_base
-aws.client.anonymous = !params.igenomes_ignore && params.igenomes_base?.startsWith('s3://ngi-igenomes/igenomes/') ?: false
 // Load nf-core custom profiles from different institutions
 
 // If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included.
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index e5c82f79d..37bfa0c7b 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -22,8 +22,8 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2025-10-16T13:39:10+00:00",
-            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new/nf-core/rnaseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.4.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/rnaseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
+            "datePublished": "2025-11-20T09:32:40+00:00",
+            "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-rnaseq_logo_dark.png\">\n    <img alt=\"nf-core/rnaseq\" src=\"docs/images/nf-core-rnaseq_logo_light.png\">\n  </picture>\n</h1>\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/rnaseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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/rnaseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnaseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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)\n\n## Introduction\n\n**nf-core/rnaseq** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n   major pipeline sections and the types of output it produces. You're giving an overview to someone new\n   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n     workflows use the \"tube map\" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n     Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/rnaseq \\\n   -profile <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnaseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnaseq/output).\n\n## Credits\n\nnf-core/rnaseq was originally written by Harshil Patel, Phil Ewels, Rickard Hammar\u00e9n.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnaseq` channel](https://nfcore.slack.com/channels/rnaseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/rnaseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
                     "@id": "main.nf"
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#9fd2026b-39c8-4f8e-94fa-5beeb4842a57"
+                    "@id": "#0ad48f19-9581-4e1b-b10f-638ab0a48482"
                 }
             ],
             "name": "nf-core/rnaseq"
@@ -128,7 +128,7 @@
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-10-16T13:39:10Z",
+            "dateModified": "2025-11-20T09:32:40Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": ["nf-core", "nextflow", "rna", "rna-seq"],
             "license": ["MIT"],
@@ -155,11 +155,11 @@
             "version": "!>=25.04.0"
         },
         {
-            "@id": "#9fd2026b-39c8-4f8e-94fa-5beeb4842a57",
+            "@id": "#0ad48f19-9581-4e1b-b10f-638ab0a48482",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#55469e2e-5231-49aa-856a-cfb378cdc6c7"
+                    "@id": "#d85e8f82-5b12-4ac5-842a-1621342f3e0b"
                 }
             ],
             "mainEntity": {
@@ -168,7 +168,7 @@
             "name": "Test suite for nf-core/rnaseq"
         },
         {
-            "@id": "#55469e2e-5231-49aa-856a-cfb378cdc6c7",
+            "@id": "#d85e8f82-5b12-4ac5-842a-1621342f3e0b",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/rnaseq",
             "resource": "repos/nf-core/rnaseq/actions/workflows/nf-test.yml",
diff --git a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
index 5304e9985..6d136061f 100644
--- a/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
@@ -39,7 +39,7 @@ workflow PIPELINE_INITIALISATION {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
@@ -64,7 +64,7 @@ workflow PIPELINE_INITIALISATION {
 \033[0;35m  nf-core/rnaseq ${workflow.manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
+    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { doi -> "    https://doi.org/${doi.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
@@ -101,7 +101,7 @@ workflow PIPELINE_INITIALISATION {
     // Create channel from input file provided through params.input
     //
 
-    Channel
+    channel
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fastq_1, fastq_2 ->
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index bfd258760..2f30e9a46 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -98,7 +98,7 @@ def workflowVersionToYAML() {
 // Get channel of software versions used in pipeline in YAML format
 //
 def softwareVersionsToYAML(ch_versions) {
-    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
+    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(channel.of(workflowVersionToYAML()))
 }
 
 //
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index 52a0dc67a..a11edd605 100644
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -22,8 +22,8 @@ workflow RNASEQ {
     ch_samplesheet // channel: samplesheet read in from --input
     main:
 
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    ch_versions = channel.empty()
+    ch_multiqc_files = channel.empty()
     //
     // MODULE: Run FastQC
     //
@@ -36,7 +36,25 @@ workflow RNASEQ {
     //
     // Collate and save software versions
     //
-    softwareVersionsToYAML(ch_versions)
+    def topic_versions = Channel.topic("versions")
+        .distinct()
+        .branch { entry ->
+            versions_file: entry instanceof Path
+            versions_tuple: true
+        }
+
+    def topic_versions_string = topic_versions.versions_tuple
+        .map { process, tool, version ->
+            [ process[process.lastIndexOf(':')+1..-1], "  ${tool}: ${version}" ]
+        }
+        .groupTuple(by:0)
+        .map { process, tool_versions ->
+            tool_versions.unique().sort()
+            "${process}:\n${tool_versions.join('\n')}"
+        }
+
+    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+        .mix(topic_versions_string)
         .collectFile(
             storeDir: "${params.outdir}/pipeline_info",
             name: 'nf_core_'  +  'rnaseq_software_'  + 'mqc_'  + 'versions.yml',
@@ -48,24 +66,24 @@ workflow RNASEQ {
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config        = Channel.fromPath(
+    ch_multiqc_config        = channel.fromPath(
         "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_custom_config = params.multiqc_config ?
-        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_config, checkIfExists: true) :
+        channel.empty()
     ch_multiqc_logo          = params.multiqc_logo ?
-        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
-        Channel.empty()
+        channel.fromPath(params.multiqc_logo, checkIfExists: true) :
+        channel.empty()
 
     summary_params      = paramsSummaryMap(
         workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_workflow_summary = channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_files = ch_multiqc_files.mix(
         ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ?
         file(params.multiqc_methods_description, checkIfExists: true) :
         file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(
+    ch_methods_description                = channel.value(
         methodsDescriptionText(ch_multiqc_custom_methods_description))
 
     ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions)

From 14f3c963090462f59ba4f4eb0dffc3c0505b658a Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 25 Nov 2025 10:39:35 +0000
Subject: [PATCH 2/5] Update CHANGELOG.md for template merge v3.5.1
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Merged with latest dev CHANGELOG entries

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 99e31128a..18c5cf94d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@ Special thanks to the following for their contributions to the release:
 - [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
 - [PR #1620](https://github.com/nf-core/rnaseq/pull/1620) - Fix bigwig strand labeling for reverse-stranded libraries ([#1591](https://github.com/nf-core/rnaseq/issues/1591))
 - [PR #1621](https://github.com/nf-core/rnaseq/pull/1621) - Optimize qualimap performance with multi-threaded name sorting
+- [PR #1628](https://github.com/nf-core/rnaseq/pull/1628) - Template update for nf-core/tools v3.5.1
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 

From f079e2a830211f1ae23d484e34a8f5596f6860f2 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 25 Nov 2025 11:12:26 +0000
Subject: [PATCH 3/5] Remove check-heatmap entries from test snapshots
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The FastQC status check heatmaps (PNG/SVG) are no longer produced
by the updated version of MultiQC from the template update

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 tests/default.nf.test.snap                  |  6 ------
 tests/featurecounts_group_type.nf.test.snap |  6 ------
 tests/hisat2.nf.test.snap                   |  6 ------
 tests/kallisto.nf.test.snap                 |  3 ---
 tests/min_mapped_reads.nf.test.snap         |  6 ------
 tests/nofasta.nf.test.snap                  |  6 ------
 tests/remove_ribo_rna.nf.test.snap          |  6 ------
 tests/salmon.nf.test.snap                   |  3 ---
 tests/sentieon_default.nf.test.snap         |  6 ------
 tests/skip_qc.nf.test.snap                  |  3 ---
 tests/skip_trimming.nf.test.snap            |  3 ---
 tests/star_rsem.nf.test.snap                |  6 ------
 tests/umi.nf.test.snap                      | 12 ------------
 13 files changed, 72 deletions(-)

diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 0798e8ef4..1e5a1b965 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -411,7 +411,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -424,7 +423,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -483,7 +481,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -496,7 +493,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -555,7 +551,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -568,7 +563,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
index 5f34e3174..2c09cabf9 100644
--- a/tests/featurecounts_group_type.nf.test.snap
+++ b/tests/featurecounts_group_type.nf.test.snap
@@ -404,7 +404,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -417,7 +416,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -474,7 +472,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -487,7 +484,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -544,7 +540,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -557,7 +552,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
index 032160724..4b599c5db 100644
--- a/tests/hisat2.nf.test.snap
+++ b/tests/hisat2.nf.test.snap
@@ -876,7 +876,6 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -889,7 +888,6 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -947,7 +945,6 @@
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/hisat2/multiqc_report_plots/png/dupradar.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -960,7 +957,6 @@
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -1018,7 +1014,6 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -1031,7 +1026,6 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
index 6fbdcc695..6eaae3964 100644
--- a/tests/kallisto.nf.test.snap
+++ b/tests/kallisto.nf.test.snap
@@ -184,7 +184,6 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -203,7 +202,6 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -222,7 +220,6 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
index 014c2f424..34a7b6827 100644
--- a/tests/min_mapped_reads.nf.test.snap
+++ b/tests/min_mapped_reads.nf.test.snap
@@ -312,7 +312,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -325,7 +324,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -385,7 +383,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -398,7 +395,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -458,7 +454,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_mapped_samples_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -471,7 +466,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap
index 8e08bc0dd..b8c1ced29 100644
--- a/tests/nofasta.nf.test.snap
+++ b/tests/nofasta.nf.test.snap
@@ -150,7 +150,6 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -163,7 +162,6 @@
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -182,7 +180,6 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
-                "multiqc/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -195,7 +192,6 @@
                 "multiqc/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -214,7 +210,6 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -227,7 +222,6 @@
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
index f6de3f886..ec96604c1 100644
--- a/tests/remove_ribo_rna.nf.test.snap
+++ b/tests/remove_ribo_rna.nf.test.snap
@@ -318,7 +318,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -331,7 +330,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -392,7 +390,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -405,7 +402,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -466,7 +462,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -479,7 +474,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
index 29e05cb9d..99ea76424 100644
--- a/tests/salmon.nf.test.snap
+++ b/tests/salmon.nf.test.snap
@@ -141,7 +141,6 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -159,7 +158,6 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -177,7 +175,6 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/sentieon_default.nf.test.snap b/tests/sentieon_default.nf.test.snap
index 69e433e8a..a49dada9b 100644
--- a/tests/sentieon_default.nf.test.snap
+++ b/tests/sentieon_default.nf.test.snap
@@ -409,7 +409,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -422,7 +421,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -481,7 +479,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -494,7 +491,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -553,7 +549,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -566,7 +561,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
index cdfc34319..807a40507 100644
--- a/tests/skip_qc.nf.test.snap
+++ b/tests/skip_qc.nf.test.snap
@@ -288,7 +288,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -322,7 +321,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -356,7 +354,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index e4e43d55b..967cbe8cd 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -262,7 +262,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -318,7 +317,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -374,7 +372,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
index 68292fc9e..ca50fa9fc 100644
--- a/tests/star_rsem.nf.test.snap
+++ b/tests/star_rsem.nf.test.snap
@@ -324,7 +324,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -337,7 +336,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -399,7 +397,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -412,7 +409,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -474,7 +470,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -487,7 +482,6 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
index 8ddd1d27c..7d76d4ca0 100644
--- a/tests/umi.nf.test.snap
+++ b/tests/umi.nf.test.snap
@@ -299,7 +299,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -312,7 +311,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -372,7 +370,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -385,7 +382,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -445,7 +441,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -458,7 +453,6 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
@@ -2266,7 +2260,6 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -2279,7 +2272,6 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
-                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -2335,7 +2327,6 @@
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/hisat2/multiqc_report_plots/png/dupradar.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -2348,7 +2339,6 @@
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
-                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -2404,7 +2394,6 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -2417,7 +2406,6 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
-                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",

From 183c47fc5570f56841a4a40d53af12b3aca88012 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 25 Nov 2025 12:59:14 +0000
Subject: [PATCH 4/5] Revert MultiQC update to v1.31 and restore test snapshots
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

MultiQC v1.32 (from the template update) no longer produces FastQC
status check heatmap PNG/PDF/SVG files, possibly related to the
Bootstrap 5 upgrade in that release.

Reverting to MultiQC v1.31 (git_sha e10b76ca0c66213581bec2833e30d31f239dec0b)
until the change in behavior is better understood, and restoring the
test snapshots that expect these files to be present.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 modules.json                                  |  4 ++--
 modules/nf-core/multiqc/environment.yml       |  2 +-
 modules/nf-core/multiqc/main.nf               |  4 ++--
 .../nf-core/multiqc/tests/main.nf.test.snap   | 24 +++++++++----------
 tests/default.nf.test.snap                    |  6 +++++
 tests/featurecounts_group_type.nf.test.snap   |  6 +++++
 tests/hisat2.nf.test.snap                     |  6 +++++
 tests/kallisto.nf.test.snap                   |  3 +++
 tests/min_mapped_reads.nf.test.snap           |  6 +++++
 tests/nofasta.nf.test.snap                    |  6 +++++
 tests/remove_ribo_rna.nf.test.snap            |  6 +++++
 tests/salmon.nf.test.snap                     |  3 +++
 tests/sentieon_default.nf.test.snap           |  6 +++++
 tests/skip_qc.nf.test.snap                    |  3 +++
 tests/skip_trimming.nf.test.snap              |  3 +++
 tests/star_rsem.nf.test.snap                  |  6 +++++
 tests/umi.nf.test.snap                        | 12 ++++++++++
 17 files changed, 89 insertions(+), 17 deletions(-)

diff --git a/modules.json b/modules.json
index a82cf3a0c..674b309c8 100644
--- a/modules.json
+++ b/modules.json
@@ -108,7 +108,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
@@ -396,7 +396,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index d02016a00..dd513cbd1 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::multiqc=1.32
+  - bioconda::multiqc=1.31
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index c1158fb08..5288f5ccf 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/8c/8c6c120d559d7ee04c7442b61ad7cf5a9e8970be5feefb37d68eeaa60c1034eb/data' :
-        'community.wave.seqera.io/library/multiqc:1.32--d58f60e4deb769bf' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ef/eff0eafe78d5f3b65a6639265a16b89fdca88d06d18894f90fcdb50142004329/data' :
+        'community.wave.seqera.io/library/multiqc:1.31--1efbafd542a23882' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index a88bafd67..17881d15c 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-27T13:33:24.356715"
+        "timestamp": "2025-09-08T20:57:36.139055243"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-27T13:34:11.103619"
+        "timestamp": "2025-09-08T20:59:15.142230631"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,737bb2c7cad54ffc2ec020791dc48b8f"
+                "versions.yml:md5,8968b114a3e20756d8af2b80713bcc4f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-27T13:34:04.615233"
+        "timestamp": "2025-09-08T20:58:29.629087066"
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 1e5a1b965..0798e8ef4 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -411,6 +411,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -423,6 +424,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -481,6 +483,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -493,6 +496,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -551,6 +555,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -563,6 +568,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
index 2c09cabf9..5f34e3174 100644
--- a/tests/featurecounts_group_type.nf.test.snap
+++ b/tests/featurecounts_group_type.nf.test.snap
@@ -404,6 +404,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -416,6 +417,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -472,6 +474,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -484,6 +487,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -540,6 +544,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -552,6 +557,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
index 4b599c5db..032160724 100644
--- a/tests/hisat2.nf.test.snap
+++ b/tests/hisat2.nf.test.snap
@@ -876,6 +876,7 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -888,6 +889,7 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -945,6 +947,7 @@
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/hisat2/multiqc_report_plots/png/dupradar.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -957,6 +960,7 @@
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -1014,6 +1018,7 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -1026,6 +1031,7 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap
index 6eaae3964..6fbdcc695 100644
--- a/tests/kallisto.nf.test.snap
+++ b/tests/kallisto.nf.test.snap
@@ -184,6 +184,7 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -202,6 +203,7 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -220,6 +222,7 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
index 34a7b6827..014c2f424 100644
--- a/tests/min_mapped_reads.nf.test.snap
+++ b/tests/min_mapped_reads.nf.test.snap
@@ -312,6 +312,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -324,6 +325,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -383,6 +385,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -395,6 +398,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -454,6 +458,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_mapped_samples_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -466,6 +471,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/nofasta.nf.test.snap b/tests/nofasta.nf.test.snap
index b8c1ced29..8e08bc0dd 100644
--- a/tests/nofasta.nf.test.snap
+++ b/tests/nofasta.nf.test.snap
@@ -150,6 +150,7 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -162,6 +163,7 @@
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -180,6 +182,7 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
+                "multiqc/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -192,6 +195,7 @@
                 "multiqc/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -210,6 +214,7 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -222,6 +227,7 @@
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap
index ec96604c1..f6de3f886 100644
--- a/tests/remove_ribo_rna.nf.test.snap
+++ b/tests/remove_ribo_rna.nf.test.snap
@@ -318,6 +318,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -330,6 +331,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -390,6 +392,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -402,6 +405,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -462,6 +466,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -474,6 +479,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap
index 99ea76424..29e05cb9d 100644
--- a/tests/salmon.nf.test.snap
+++ b/tests/salmon.nf.test.snap
@@ -141,6 +141,7 @@
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -158,6 +159,7 @@
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -175,6 +177,7 @@
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/sentieon_default.nf.test.snap b/tests/sentieon_default.nf.test.snap
index a49dada9b..69e433e8a 100644
--- a/tests/sentieon_default.nf.test.snap
+++ b/tests/sentieon_default.nf.test.snap
@@ -409,6 +409,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -421,6 +422,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -479,6 +481,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -491,6 +494,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -549,6 +553,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -561,6 +566,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap
index 807a40507..cdfc34319 100644
--- a/tests/skip_qc.nf.test.snap
+++ b/tests/skip_qc.nf.test.snap
@@ -288,6 +288,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -321,6 +322,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -354,6 +356,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index 967cbe8cd..e4e43d55b 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -262,6 +262,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -317,6 +318,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -372,6 +374,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap
index ca50fa9fc..68292fc9e 100644
--- a/tests/star_rsem.nf.test.snap
+++ b/tests/star_rsem.nf.test.snap
@@ -324,6 +324,7 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -336,6 +337,7 @@
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -397,6 +399,7 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -409,6 +412,7 @@
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -470,6 +474,7 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -482,6 +487,7 @@
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
diff --git a/tests/umi.nf.test.snap b/tests/umi.nf.test.snap
index 7d76d4ca0..8ddd1d27c 100644
--- a/tests/umi.nf.test.snap
+++ b/tests/umi.nf.test.snap
@@ -299,6 +299,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -311,6 +312,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -370,6 +372,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -382,6 +385,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -441,6 +445,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -453,6 +458,7 @@
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",
@@ -2260,6 +2266,7 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/dupradar.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf",
@@ -2272,6 +2279,7 @@
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
+                "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf",
                 "multiqc/hisat2/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf",
@@ -2327,6 +2335,7 @@
                 "multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png",
                 "multiqc/hisat2/multiqc_report_plots/png/dupradar.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png",
@@ -2339,6 +2348,7 @@
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png",
+                "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png",
                 "multiqc/hisat2/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png",
@@ -2394,6 +2404,7 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/dupradar.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg",
@@ -2406,6 +2417,7 @@
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg",
+                "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg",
                 "multiqc/hisat2/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg",

From a09ac0c21027a20a8bdabcca5773a940f3e2a432 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 25 Nov 2025 13:07:35 +0000
Subject: [PATCH 5/5] Update utils_nfcore_pipeline subworkflow to template
 v3.5.1

The template merge updated this subworkflow but it was incorrectly reverted along with MultiQC. This commit updates only the utils_nfcore_pipeline git_sha to the v3.5.1 version while keeping MultiQC at v1.31.
---
 modules.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 674b309c8..0181969c9 100644
--- a/modules.json
+++ b/modules.json
@@ -396,7 +396,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {