Template update

.github/actions/nf-test/action.yml

@@ -20,12 +20,12 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
       with:
         python-version: "3.14"
 
@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10
+      - uses: actions/stale@4391f3da665fdf50b6810c1a66712fb9ba21aa93 # v11
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/download_pipeline.yml

@@ -39,15 +39,15 @@ jobs:
     needs: configure
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"

.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@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,12 +32,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       # Install and run prek
       - name: Run prek
         id: prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
         continue-on-error: true
 
       # indication that the linting has finished

.github/workflows/linting.yml

@@ -11,30 +11,30 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
       - name: Run prek
-        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
+        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
+        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
 
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
         with:
           python-version: "3.14"
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
@@ -46,7 +46,7 @@ jobs:
         run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
+        if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/nf-test.yml

@@ -40,7 +40,7 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
           ls -la ./
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 
@@ -86,7 +86,7 @@ jobs:
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
 
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           fetch-depth: 0
 

.github/workflows/release-announcements.yml

@@ -18,7 +18,7 @@ jobs:
         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
-      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
+      - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)

.github/workflows/template-version-comment.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
         with:
           ref: ${{ github.event.pull_request.head.sha }}
 

.hooks/block_pipeline_outdir.sh

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+# This hook is used to block commits if they include staged files inside a directory
+# which also contains a subdirectory called `pipeline_info`. The purpose of this is to
+# prevent users from inadvertently committing output from pipeline test runs inside the
+# development directory.
+
+set -e
+
+status=0
+seen_dirs=""
+
+while IFS= read -r file; do
+    # The offending output bundle's root is the ancestor directory that has
+    # `pipeline_info` as an immediate child, so callers can restore it in one go.
+    if [[ "$file" == pipeline_info/* ]]; then
+        top_dir="pipeline_info"
+    elif [[ "$file" == */pipeline_info/* ]]; then
+        top_dir="${file%%/pipeline_info/*}"
+    else
+        top_dir=""
+        dir=$(dirname "$file")
+        while [[ "$dir" != "." && "$dir" != "/" ]]; do
+            if [[ -d "$dir/pipeline_info" ]]; then
+                top_dir="$dir"
+                break
+            fi
+            dir=$(dirname "$dir")
+        done
+    fi
+
+    if [[ -n "$top_dir" ]]; then
+        echo "❌ Commit blocked: Please do not commit output from pipeline test runs to the pipeline code itself: $file"
+        status=1
+        case "$seen_dirs" in
+            *"|$top_dir|"*) ;;
+            *)
+                echo "Run 'git restore --staged $top_dir' to remove the whole output folder from the staging area."
+                seen_dirs="$seen_dirs|$top_dir|"
+                ;;
+        esac
+    fi
+done < <(git diff --cached --name-only)
+
+exit "$status"

.nf-core.yml

@@ -12,7 +12,7 @@ lint:
     - docs/images/nf-core-spatialvi_logo_dark.png
     - .github/workflows/branch.yml
     - .github/workflows/linting.yml
-nf_core_version: 4.0.2
+nf_core_version: 4.1.0
 repository_type: pipeline
 template:
   author: Erik Fasterius, Christophe Avenel, Sergii Domanskyi, Jeffrey Chuang, Anuj Srivastava

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.8.3
+          - prettier@3.9.6
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -25,9 +25,26 @@ repos:
               subworkflows/(?!local/).*|
               .*\.snap$
           )$
+      - id: check-added-large-files
+        args: [--maxkb=5000]
+        exclude: |
+          (?x)^(
+              .*ro-crate-metadata.json$|
+              .*\.snap$|
+              lib/nfcore_external_java_deps.jar$|
+              docs/.*\.(svg|pdf)$|
+              assets/.*$
+          )$
+      - id: check-merge-conflict
   - repo: https://github.com/seqeralabs/nf-lint-pre-commit
     rev: v0.3.0
     hooks:
       - id: nextflow-lint
         files: '\.nf$|nextflow\.config$'
         args: ["-output", "json"]
+  - repo: local
+    hooks:
+      - id: block-pipeline-outdir
+        name: Prevent committing output from pipeline test runs to the pipeline code itself
+        entry: ./.hooks/block_pipeline_outdir.sh
+        language: script

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## v1.0dev - [unreleased<!-- TODO nf-core: replace with date on release -->]
 
 Initial release of nf-core/spatialvi, created with the
 [nf-core](https://nf-co.re/) template. This marks the point at which the

README.md

@@ -11,7 +11,7 @@
 [![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%A525.10.4-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-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)
 [![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/)

conf/base.config

@@ -42,6 +42,9 @@ process {
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
     }
+    withLabel:process_low_memory {
+        memory = { 1.GB * task.attempt }
+    }
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }

conf/containers_conda_lock_files_amd64.config

@@ -1,2 +1,2 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt' } }
+process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-c17fb751507e9dfc_1.txt' } }

conf/containers_conda_lock_files_arm64.config

@@ -1,2 +1,2 @@
-process { withName: 'FASTQC' { container = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
-process { withName: 'MULTIQC' { container = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt' } }
+process { withName: 'FASTQC' { conda = 'modules/nf-core/fastqc/.conda-lock/linux_arm64-bd-e455e32f745abe68_1.txt' } }
+process { withName: 'MULTIQC' { conda = 'modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-5c84a5000a226ab5_1.txt' } }

conf/containers_docker_amd64.config

@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2' } }
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--c17fb751507e9dfc' } }

conf/containers_docker_arm64.config

@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68' } }
-process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
+process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.35--5c84a5000a226ab5' } }

conf/containers_singularity_https_amd64.config

@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f2/f20b021476d1d87658820f971ebecc1e8cdbde0f338eb0d9cea2b0a8fc54a54b/data' } }
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8e346f4f6080eadf1253505e6ff09ef004454fc18e8d672006fd7b222cc412e/data' } }

conf/containers_singularity_https_arm64.config

@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46daf2dad0169afd2ae047c3e50ed3776259f664bf07e5e06b045dc23449e994/data' } }
-process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
+process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e4/e48aa28aebc881254a499b24c3e1ce77b8df1b85a5432699ed6f72eb17ac7fb5/data' } }

conf/containers_singularity_oras_amd64.config

@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--5c4bd442468d75dd' } }
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c680f2aea25ccec2' } }

conf/containers_singularity_oras_arm64.config

@@ -1,2 +1,2 @@
 process { withName: 'FASTQC' { container = 'oras://community.wave.seqera.io/library/fastqc:0.12.1--127a87fc06499035' } }
-process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
+process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.35--c0468833d65b2f81' } }

conf/modules.config

@@ -75,23 +75,19 @@ process {
         ext.args = { "--metadata subtitle:'Sample: ${meta.id}'" }
         container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef'
         publishDir = [
-            [
-                path: { "${params.outdir}/${meta.id}/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "*{.html,.qmd,_extensions}"
-            ],
-            [
-                path: { "${params.outdir}/${meta.id}/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "params.yml",
-                saveAs: { "${notebook.baseName}.yml" }
-            ],
-            [
-                path: { "${params.outdir}/${meta.id}/plots" },
-                mode: params.publish_dir_mode,
-                pattern: "artifacts/*.png",
-                saveAs: { filename -> filename.split('/')[1] }
-            ]
+            path: { "${params.outdir}/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename ==~ /.*\.(html|qmd)$/ || filename.endsWith('_extensions')) {
+                    "reports/${filename}"
+                } else if (filename == 'params.yml') {
+                    "reports/${notebook.baseName}.yml"
+                } else if (filename.startsWith('artifacts/') && filename.endsWith('.png')) {
+                    "plots/${filename.split('/')[1]}"
+                } else {
+                    null
+                }
+            }
         ]
     }
 
@@ -124,23 +120,19 @@ process {
         ext.prefix = { "${notebook.baseName}" }
         container = 'community.wave.seqera.io/library/harmonypy_scanorama_gcc_gxx_pruned:95f731fde0b9ddef'
         publishDir = [
-            [
-                path: { "${params.outdir}/integration/reports"},
-                mode: params.publish_dir_mode,
-                pattern: "*{.html,.qmd,_extensions}"
-            ],
-            [
-                path: { "${params.outdir}/integration/reports" },
-                mode: params.publish_dir_mode,
-                pattern: "params.yml",
-                saveAs: { "${notebook.baseName}.yml" }
-            ],
-            [
-                path: { "${params.outdir}/integration/plots" },
-                mode: params.publish_dir_mode,
-                pattern: "artifacts/*.png",
-                saveAs: { filename -> filename.split('/')[1] }
-            ]
+            path: { "${params.outdir}/integration" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename ->
+                if (filename ==~ /.*\.(html|qmd)$/ || filename.endsWith('_extensions')) {
+                    "reports/${filename}"
+                } else if (filename == 'params.yml') {
+                    "reports/${notebook.baseName}.yml"
+                } else if (filename.startsWith('artifacts/') && filename.endsWith('.png')) {
+                    "plots/${filename.split('/')[1]}"
+                } else {
+                    null
+                }
+            }
         ]
     }