dev -> main for 3.5.0

.devcontainer/build-devcontainer/Dockerfile

@@ -1,6 +1,6 @@
 # devcontainers/miniconda image based on debian (bookworm)
 # see tags and images: https://mcr.microsoft.com/en-us/artifact/mar/devcontainers/miniconda/tags
-FROM "mcr.microsoft.com/devcontainers/miniconda@sha256:8e262a2664fab1d53054738d3633338558a2078ce66d3abde55c130f0d5da94f" AS build
+FROM mcr.microsoft.com/devcontainers/miniconda@sha256:19516babd35bccd1429591a255dd867b2c8c01606cc594a8a6fe5db03309ecf8 AS build
 
 # copy this repo at current revision
 COPY . /root/nfcore-tools/
@@ -27,7 +27,7 @@ RUN apt-get update --quiet && \
     rm -rf /var/lib/apt/lists/*
 
 # Final stage to copy only the required files after installation
-FROM "mcr.microsoft.com/devcontainers/base:debian@sha256:ce2e9e611939e611b737362c045bb6d3449bb3efb84898525d724aace1737b90" AS final
+FROM mcr.microsoft.com/devcontainers/base:debian@sha256:2e826a6ae92e5744cc0a471a03b4411e64f6b7cc6af3adaecddad697f0018f10 AS final
 
 # Copy only the conda environment and site-packages from build stage
 COPY --from=build /opt/conda /opt/conda

.devcontainer/devcontainer.json

@@ -1,6 +1,6 @@
 {
     "name": "nfcore",
-    "image": "nfcore/devcontainer:latest",
+    "image": "nfcore/devcontainer:dev",
 
     "remoteEnv": {
         // Workspace path on the host for mounting with docker-outside-of-docker

.devcontainer/setup.sh

@@ -9,5 +9,8 @@ export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 # Update Nextflow
 nextflow self-update
 
+# Install specifically the version of tools from the workspace
+pip install --upgrade  -r requirements.txt -r requirements-dev.txt -e .
+
 # Update welcome message
 echo "Welcome to the nf-core devcontainer!" > /usr/local/etc/vscode-dev-containers/first-run-notice.txt

.github/RELEASE_CHECKLIST.md

@@ -4,7 +4,7 @@
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
 4. Check that modules/subworkflows in template are up to date with the latest releases
-5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:latest`.
+5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py`.
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `main`
 8. Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR: use the `Sync template` GitHub Action from the tools repository specifying the pipeline name and running from the `dev` branch.
@@ -22,4 +22,4 @@
 3. Manually trigger the `Sync template` GitHub Action for all pipelines.
 4. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 5. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py` and change the `.devcontainer/devcontainer.json` container to `nfcore/gitpod:dev`.
+6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `setup.py`.

.github/actions/create-lint-wf/action.yml

@@ -82,7 +82,7 @@ runs:
 
     - name: Upload log file artifact
       if: ${{ always() }}
-      uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+      uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
       with:
         name: nf-core-log-file-${{ matrix.NXF_VER }}
         path: create-lint-wf/log.txt

.github/snapshots/adaptivecard.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
     }
-}
+}

.github/snapshots/changelog.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:01.993722854"
     }
-}
+}

.github/snapshots/ci.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:03.306256217"
     }
-}
+}

.github/snapshots/citations.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
     }
-}
+}

.github/snapshots/code_linters.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
     }
-}
+}

.github/snapshots/codespaces.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:14.716393995"
     }
-}
+}

.github/snapshots/default.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:29:04.284923"
     }
-}
+}

.github/snapshots/documentation.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
     }
-}
+}

.github/snapshots/email.nf.test.snap

@@ -47,7 +47,6 @@
                 "multiqc/multiqc_data/multiqc_sources.txt",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_plots/pdf",
-                "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf",
@@ -60,7 +59,6 @@
                 "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf",
                 "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf",
                 "multiqc/multiqc_plots/png",
-                "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png",
                 "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png",
@@ -73,7 +71,6 @@
                 "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png",
                 "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png",
                 "multiqc/multiqc_plots/svg",
-                "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg",
                 "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg",
                 "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg",
@@ -111,4 +108,4 @@
         },
         "timestamp": "2025-05-07T13:52:10.350817122"
     }
-}
+}