diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 3b9724c7..a34abe8e 100644 --- a/.github/actions/nf-test/action.yml +++ b/.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') diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 9a789de4..b1fcf88e 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -2,11 +2,13 @@ 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 @@ -14,33 +16,47 @@ jobs: # 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 < 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: ${{ always() }} + uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7 + with: + name: pr-comment + path: pr-comment/ diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml deleted file mode 100644 index 5b0c24f7..00000000 --- a/.github/workflows/linting_comment.yml +++ /dev/null @@ -1,28 +0,0 @@ -name: nf-core linting comment -# This workflow is triggered after the linting action is complete -# It posts an automated comment to the PR, even if the PR is coming from a fork - -on: - workflow_run: - workflows: ["nf-core linting"] - -jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Download lint results - uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21 - with: - workflow: linting.yml - workflow_conclusion: completed - - - name: Get PR number - id: pr_number - run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - - - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - number: ${{ steps.pr_number.outputs.pr_number }} - path: linting-logs/lint_results.md diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 431d3d44..abc44c92 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -18,7 +18,7 @@ jobs: id: get_description run: | echo "description=$(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: ${{ secrets.MASTODON_ACCESS_TOKEN }} host: "mstdn.science" # custom host if not "mastodon.social" (default) diff --git a/.nf-core.yml b/.nf-core.yml index bcea0e92..43484e56 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -10,7 +10,7 @@ lint: - docs/images/nf-core-spatialaxe_logo_dark.png - docs/images/nf-core-spatialaxe_logo_light.png - .github/PULL_REQUEST_TEMPLATE.md -nf_core_version: 4.0.2 +nf_core_version: 4.0.3 repository_type: pipeline template: author: Sameesh Kher, Dongze He, Florian Heyl diff --git a/CHANGELOG.md b/CHANGELOG.md index b960e927..b18a6d84 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,7 +9,7 @@ Hotfix to tackle some bugs ### `Added` -- Template update for nf-core/tools version 4.0.2 +- Template update for nf-core/tools version 4.0.3 ### `Fixed` diff --git a/main.nf b/main.nf index ed5c9d42..dbbb24d4 100644 --- a/main.nf +++ b/main.nf @@ -135,7 +135,6 @@ workflow { params.plaintext_email, params.outdir, params.monochrome_logs, - params.hook_url, NFCORE_SPATIALAXE.out.multiqc_report ) } diff --git a/nextflow.config b/nextflow.config index eef01269..6e5a571b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -290,11 +290,13 @@ profiles { } -// Load nf-core custom profiles from different institutions │ +// If params.custom_config_base is set AND either the NXF_OFFLINE environment variable is not set or params.custom_config_base is a local path, the nfcore_custom.config file from the specified base path is included. +// Load nf-core/spatialaxe custom profiles from different institutions. includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${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. diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 0a88ac08..2ac72fc8 100644 --- a/ro-crate-metadata.json +++ b/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", diff --git a/subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf b/subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf index fda9b46e..6f230ef0 100644 --- a/subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf +++ b/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"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • 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
    • " - ].join(' ').trim() + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • 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
    • " + ].join(' ').trim() return reference_text } diff --git a/tests/nextflow.config b/tests/nextflow.config index 2c1bfd32..5a98fc21 100644 --- a/tests/nextflow.config +++ b/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