Solve merge conflict template 4.0.3

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

@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@main
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')

.github/workflows/branch.yml

@@ -2,45 +2,61 @@ name: nf-core branch protection
 # This workflow is triggered on PRs to `main`/`master` branch on the repository
 # It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
 on:
-  pull_request_target:
+  pull_request:
     branches:
       - main
       - master
 
+permissions: {}
+
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
       # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'nf-core/spatialaxe'
+        env:
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/spatialaxe ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ "$HEAD_REPO" == nf-core/spatialaxe ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
-      # If the above check failed, post a comment on the PR explaining the failure
-      # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
-      - name: Post PR comment
+      # If the above check failed, build a comment to be posted by the shared poster workflow
+      - name: Build PR comment
         if: failure()
-        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
-        with:
-          message: |
-            ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          BASE_REF: ${{ github.event.pull_request.base.ref }}
+          HEAD_REPO: ${{ github.event.pull_request.head.repo.full_name }}
+          PR_USER: ${{ github.event.pull_request.user.login }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "branch" > pr-comment/header.txt
+          cat > pr-comment/comment.md <<EOF
+          ## This PR is against the \`${BASE_REF}\` branch :x:
 
-            * Do not close this PR
-            * Click _Edit_ and change the `base` to `dev`
-            * This CI test will remain failed until you push a new commit
+          * Do not close this PR
+          * Click _Edit_ and change the \`base\` to \`dev\`
+          * This CI test will remain failed until you push a new commit
 
-            ---
+          ---
 
-            Hi @${{ github.event.pull_request.user.login }},
+          Hi @${PR_USER},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
-            The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+          It looks like this pull-request is has been made against the [${HEAD_REPO}](https://github.com/${HEAD_REPO}) ${BASE_REF} branch.
+          The ${BASE_REF} branch on nf-core repositories should always contain code from the latest release.
+          Because of this, PRs to ${BASE_REF} are only allowed if they come from the [${HEAD_REPO}](https://github.com/${HEAD_REPO}) \`dev\` branch.
 
-            You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
-            Note that even after this, the test will continue to show as failing until you push a new commit.
+          You do not need to close this PR, you can change the target branch to \`dev\` by clicking the _"Edit"_ button at the top of this page.
+          Note that even after this, the test will continue to show as failing until you push a new commit.
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+          Thanks again for your contribution!
+          EOF
+
+      - name: Upload PR comment artifact
+        if: failure()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/

.github/workflows/linting.yml

@@ -74,3 +74,21 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+
+      # Build a comment for the shared pr-comment.yml poster to publish on the PR
+      - name: Prepare PR comment
+        if: ${{ always() }}
+        env:
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+        run: |
+          mkdir -p pr-comment
+          echo "$PR_NUMBER" > pr-comment/pr_number.txt
+          echo "lint" > pr-comment/header.txt
+          [ -f lint_results.md ] && cp lint_results.md pr-comment/comment.md || true
+
+      - name: Upload PR comment artifact
+        if: ${{ always() }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: pr-comment
+          path: pr-comment/

.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@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)

.nf-core.yml

@@ -10,7 +10,7 @@ lint:
     - docs/images/nf-core-spatialaxe_logo_dark.png
     - docs/images/nf-core-spatialaxe_logo_light.png
     - .github/PULL_REQUEST_TEMPLATE.md
-nf_core_version: 4.0.2
+nf_core_version: 4.0.3
 repository_type: pipeline
 template:
   author: Sameesh Kher, Dongze He, Florian Heyl

CHANGELOG.md

@@ -9,7 +9,7 @@ Hotfix to tackle some bugs
 
 ### `Added`
 
-- Template update for nf-core/tools version 4.0.2
+- Template update for nf-core/tools version 4.0.3
 
 ### `Fixed`
 

main.nf

@@ -135,7 +135,6 @@ workflow {
         params.plaintext_email,
         params.outdir,
         params.monochrome_logs,
-        params.hook_url,
         NFCORE_SPATIALAXE.out.multiqc_report
     )
 }

nextflow.config

@@ -290,11 +290,13 @@ profiles {
 }
 
 
-// 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.
+// Load nf-core/spatialaxe custom profiles from different institutions.
 includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
+
 // Load nf-core/spatialaxe custom profiles from different institutions.
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/spatialaxe.config" : "/dev/null"
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/spatialaxe.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -305,6 +307,8 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
+
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.

ro-crate-metadata.json

@@ -136,6 +136,9 @@
                 {
                     "@id": "https://orcid.org/0009-0008-2420-6464"
                 },
+                {
+                    "@id": "#5fd4466e-7ce2-4d27-924e-ee46d6d24240"
+                },
                 {
                     "@id": "https://orcid.org/0000-0002-3651-5685"
                 }
@@ -360,6 +363,11 @@
             "name": "Sameesh Kher",
             "url": "https://github.com/khersameesh24"
         },
+        {
+            "@id": "#5fd4466e-7ce2-4d27-924e-ee46d6d24240",
+            "@type": "Person",
+            "name": "Dongze He"
+        },
         {
             "@id": "https://orcid.org/0000-0002-3651-5685",
             "@type": "Person",

subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf

@@ -8,14 +8,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap        } from 'plugin/nf-schema'
-include { samplesheetToList       } from 'plugin/nf-schema'
-include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
-include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
-include { imNotification          } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE   } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
+include { UTILS_NFSCHEMA_PLUGIN     } from '../../nf-core/utils_nfschema_plugin'
+include { paramsSummaryMap          } from 'plugin/nf-schema'
+include { samplesheetToList         } from 'plugin/nf-schema'
+include { paramsHelp                } from 'plugin/nf-schema'
+include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
+include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
+include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -63,6 +63,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
+
+    def before_text = ""
+    def after_text = ""
     before_text = """
 -\033[2m----------------------------------------------------\033[0m-
                                         \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
@@ -166,7 +169,6 @@ workflow PIPELINE_COMPLETION {
     plaintext_email // boolean: Send plain-text email instead of HTML
     outdir          //    path: Path to output directory where results will be published
     monochrome_logs // boolean: Disable ANSI colour codes in log output
-    hook_url        //  string: hook URL for notifications
     multiqc_report  //  string: Path to MultiQC report
 
     main:
@@ -190,13 +192,11 @@ workflow PIPELINE_COMPLETION {
         }
 
         completionSummary(monochrome_logs)
-        if (hook_url) {
-            imNotification(summary_params, hook_url)
-        }
+
     }
 
     workflow.onError {
-        error("❌ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting")
+        log.error "Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting"
     }
 }
 
@@ -294,23 +294,27 @@ def validateInputParameters(
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
+    // TODO nf-core: Optionally add in-text citation tools to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
-        "Tools used in the workflow included:",
-        "MultiQC (Ewels et al. 2016)",
-        ".",
-    ].join(' ').trim()
+            "Tools used in the workflow included:",
+            "FastQC (Andrews 2010),",
+            "MultiQC (Ewels et al. 2016)",
+            "."
+        ].join(' ').trim()
 
     return citation_text
 }
 
 def toolBibliographyText() {
+    // TODO nf-core: Optionally add bibliographic entries to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-        "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
-    ].join(' ').trim()
+            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
+            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>"
+        ].join(' ').trim()
 
     return reference_text
 }

tests/nextflow.config

@@ -7,7 +7,7 @@
 // Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
-    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/spatialaxe'
+    pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/spatialaxe/'
 }
 
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners