diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 243e782..bf44d96 100644 --- a/.github/actions/nf-test/action.yml +++ b/.github/actions/nf-test/action.yml @@ -54,13 +54,9 @@ runs: conda-solver: libmamba conda-remove-defaults: true - # TODO Skip failing conda tests and document their failures - # https://github.com/nf-core/modules/issues/7017 - name: Run nf-test shell: bash env: - NFT_DIFF: ${{ env.NFT_DIFF }} - NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} NFT_WORKDIR: ${{ env.NFT_WORKDIR }} run: | nf-test test \ diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index f2d7d1d..8b0f88c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - - name: Set up Python 3.12 + - name: Set up Python 3.13 uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5 with: python-version: "3.13" diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 7e8050f..d43797d 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index f03aea0..e7b5844 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -1,12 +1,5 @@ name: Run nf-test on: - push: - paths-ignore: - - "docs/**" - - "**/meta.yml" - - "**/*.md" - - "**/*.png" - - "**/*.svg" pull_request: paths-ignore: - "docs/**" @@ -35,7 +28,7 @@ jobs: nf-test-changes: name: nf-test-changes runs-on: # use self-hosted runners - - runs-on=$-nf-test-changes + - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64 outputs: shard: ${{ steps.set-shards.outputs.shard }} @@ -69,7 +62,7 @@ jobs: needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} runs-on: # use self-hosted runners - - runs-on=$-nf-test + - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64 strategy: fail-fast: false @@ -85,7 +78,7 @@ jobs: - isMain: false profile: "singularity" NXF_VER: - - "24.04.2" + - "24.10.5" - "latest-everything" env: NXF_ANSI_LOG: false @@ -97,23 +90,39 @@ jobs: fetch-depth: 0 - name: Run nf-test + id: run_nf_test uses: ./.github/actions/nf-test + continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }} env: - NFT_DIFF: ${{ env.NFT_DIFF }} - NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} NFT_WORKDIR: ${{ env.NFT_WORKDIR }} with: profile: ${{ matrix.profile }} shard: ${{ matrix.shard }} total_shards: ${{ env.TOTAL_SHARDS }} + + - name: Report test status + if: ${{ always() }} + run: | + if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then + echo "::error::Test with ${{ matrix.NXF_VER }} failed" + # Add to workflow summary + echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY + if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then + echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing." + fi + if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + exit 1 + fi + fi + confirm-pass: needs: [nf-test] if: always() runs-on: # use self-hosted runners - - runs-on=$-confirm-pass + - runs-on=${{ github.run_id }}-confirm-pass - runner=2cpu-linux-x64 steps: - - name: One or more tests failed + - name: One or more tests failed (excluding latest-everything) if: ${{ contains(needs.*.result, 'failure') }} run: exit 1 @@ -132,11 +141,3 @@ jobs: echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" echo "::endgroup::" - - - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner - if: always() - run: | - ls -la ./ - rm -rf ./* || true - rm -rf ./.??* || true - ls -la ./ diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 4abaf48..0f73249 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -30,7 +30,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0 + - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.nf-core.yml b/.nf-core.yml index 95bac5c..cc42028 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,4 @@ -nf_core_version: 3.3.1 +nf_core_version: 3.3.2 repository_type: pipeline template: author: Christopher Hakkaart @@ -8,4 +8,4 @@ template: name: demo org: nf-core outdir: . - version: 1.0.0 + version: 1.0.2 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9d0b248..bb41bee 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -4,7 +4,7 @@ repos: hooks: - id: prettier additional_dependencies: - - prettier@3.5.0 + - prettier@3.6.2 - repo: https://github.com/pre-commit/pre-commit-hooks rev: v5.0.0 hooks: diff --git a/CHANGELOG.md b/CHANGELOG.md index 55f7175..b8027cb 100644 --- a/CHANGELOG.md +++ b/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). -## v1.0.0 - [date] +## v1.0.2 - [date] Initial release of nf-core/demo, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index b207f50..5415bc1 100644 --- a/README.md +++ b/README.md @@ -5,12 +5,12 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1) +[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2) [![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/assets/multiqc_config.yml b/assets/multiqc_config.yml index 1a9c348..dd180e7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/demo + This report has been generated by the nf-core/demo analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-demo-methods-description": order: -1000 diff --git a/assets/schema_input.json b/assets/schema_input.json index af0934a..58bebb9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -17,14 +17,14 @@ "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, diff --git a/conf/base.config b/conf/base.config index f76c4d3..938165b 100644 --- a/conf/base.config +++ b/conf/base.config @@ -61,5 +61,6 @@ process { } withLabel: process_gpu { ext.use_gpu = { workflow.profile.contains('gpu') } + accelerator = { workflow.profile.contains('gpu') ? 1 : null } } } diff --git a/modules.json b/modules.json index 1974b10..1061a1a 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c7..f9f54ee 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 033f415..23e1663 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,7 @@ process FASTQC { // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null + def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 2b2e62b..c8d9d02 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -29,9 +29,10 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + ontologies: [] output: - - html: - - meta: + html: + - - meta: type: map description: | Groovy Map containing sample information @@ -40,8 +41,9 @@ output: type: file description: FastQC report pattern: "*_{fastqc.html}" - - zip: - - meta: + ontologies: [] + zip: + - - meta: type: map description: | Groovy Map containing sample information @@ -50,11 +52,14 @@ output: type: file description: FastQC report archive pattern: "*_{fastqc.zip}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122c..812fc4c 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,5 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.27 + - bioconda::multiqc=1.29 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 58d9313..0ac3c36 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : - 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : + 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index b16c187..ce30eb7 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -15,57 +15,71 @@ tools: licence: ["GPL-3.0-or-later"] identifier: biotools:multiqc input: - - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - - - multiqc_logo: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + ontologies: [] + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + ontologies: [] + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" + ontologies: + - edam: http://edamontology.org/format_3475 # TSV +output: + report: + - "*multiqc_report.html": type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: + description: MultiQC report file + pattern: "multiqc_report.html" + ontologies: [] + data: + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" + plots: + - "*_plots": type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: + description: Plots created by MultiQC + pattern: "*_data" + ontologies: [] + versions: + - versions.yml: type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" -output: - - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7b7c132..88e9057 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:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:29:57.631982377" + "timestamp": "2025-05-22T11:50:41.182332996" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:34.743726958" + "timestamp": "2025-05-22T11:51:22.448739369" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" + "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.2" }, - "timestamp": "2025-01-27T09:30:21.44383553" + "timestamp": "2025-05-22T11:51:06.198928424" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 952e5f9..9d6c221 100644 --- a/nextflow.config +++ b/nextflow.config @@ -235,7 +235,6 @@ dag { manifest { name = 'nf-core/demo' - author = """Christopher Hakkaart""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ @@ -251,14 +250,14 @@ manifest { description = """An nf-core demo pipeline""" mainScript = 'main.nf' defaultBranch = 'master' - nextflowVersion = '!>=24.04.2' - version = '1.0.0' + nextflowVersion = '!>=24.10.5' + version = '1.0.2' doi = '' } // Nextflow plugins plugins { - id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.4.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/nf-test.config b/nf-test.config index 889df76..3a1fff5 100644 --- a/nf-test.config +++ b/nf-test.config @@ -9,7 +9,7 @@ config { configFile "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*' + ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' // run all test with defined profile(s) from the main nextflow.config profile "test" diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index f0bd6b8..9aba009 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2025-06-03T11:01:08+00:00", - "description": "

\n \n \n \"nf-core/demo\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/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%A524.04.2-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-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** is a bioinformatics pipeline that ...\n\n\n\n\n1. 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\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/demo \\\n -profile \\\n --input samplesheet.csv \\\n --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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Christopher Hakkaart.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\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": "2025-07-08T11:39:03+00:00", + "description": "

\n \n \n \"nf-core/demo\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/demo/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/demo/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/demo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/demo/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/demo/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%A524.10.5-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\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/demo)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![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/demo** is a bioinformatics pipeline that ...\n\n\n\n\n1. 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\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/demo \\\n -profile \\\n --input samplesheet.csv \\\n --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/demo/usage) and the [parameter documentation](https://nf-co.re/demo/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/demo/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/demo/output).\n\n## Credits\n\nnf-core/demo was originally written by Christopher Hakkaart.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\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 `#demo` channel](https://nfcore.slack.com/channels/demo) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\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": "#45209ed9-bae4-4876-89b4-505c8ca5d932" + "@id": "#246b126d-c3e5-4139-91d8-0c1a4138213f" } ], "name": "nf-core/demo" @@ -123,7 +123,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-06-03T11:01:08Z", + "dateModified": "2025-07-08T11:39:03Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": ["nf-core", "nextflow", "demo", "minimal-example", "training", "tutorial"], "license": ["MIT"], @@ -134,8 +134,8 @@ "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/1.0.0/"], - "version": ["1.0.0"] + "url": ["https://github.com/nf-core/demo", "https://nf-co.re/demo/1.0.2/"], + "version": ["1.0.2"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -147,14 +147,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.04.2" + "version": "!>=24.10.5" }, { - "@id": "#45209ed9-bae4-4876-89b4-505c8ca5d932", + "@id": "#246b126d-c3e5-4139-91d8-0c1a4138213f", "@type": "TestSuite", "instance": [ { - "@id": "#bc540ef0-e713-48bd-8bd6-960f63f3edda" + "@id": "#ffafd653-8724-44e6-becc-7ba2b8d6d6ae" } ], "mainEntity": { @@ -163,7 +163,7 @@ "name": "Test suite for nf-core/demo" }, { - "@id": "#bc540ef0-e713-48bd-8bd6-960f63f3edda", + "@id": "#ffafd653-8724-44e6-becc-7ba2b8d6d6ae", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/demo", "resource": "repos/nf-core/demo/actions/workflows/nf-test.yml", diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 0907ac5..09ef842 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -1,5 +1,5 @@ plugins { - id "nf-schema@2.1.0" + id "nf-schema@2.4.2" } validation { diff --git a/tests/.nftignore b/tests/.nftignore index c10bc1f..158c83c 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,5 +1,6 @@ .DS_Store multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt +multiqc/multiqc_data/BETA-multiqc.parquet multiqc/multiqc_data/multiqc.log multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_sources.txt diff --git a/tests/nextflow.config b/tests/nextflow.config index 783f100..db709dd 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -6,7 +6,9 @@ // TODO nf-core: Specify any additional parameters here // Or any resources requirements -params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' -params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/demo' +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/demo' +} aws.client.anonymous = true // fixes S3 access issues on self-hosted runners