diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml index d453dc930..ea815a219 100644 --- a/.github/workflows/sync.yml +++ b/.github/workflows/sync.yml @@ -1,7 +1,7 @@ name: Sync template on: - release: - types: [published] + # release: + # types: [published] workflow_dispatch: inputs: testpipeline: @@ -39,7 +39,7 @@ jobs: run: | if [ "${{ github.event.inputs.testpipeline }}" == "true" ]; then echo '{"pipeline":["testpipeline"]}' > pipeline_names.json - elif [ "${{ github.event.inputs.pipeline }}" != "all" ]; then + elif [ "${{ github.event.inputs.pipeline }}" != "all" ] && [ "${{ github.event.inputs.pipeline }}" != "" ]; then curl -O https://nf-co.re/pipeline_names.json # check if the pipeline exists if ! grep -q "\"${{ github.event.inputs.pipeline }}\"" pipeline_names.json; then diff --git a/CHANGELOG.md b/CHANGELOG.md index 928696f9c..5ad584d68 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,23 @@ # nf-core/tools: Changelog +## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] + +### Template + +- Add null/ to .gitignore ([#3191](https://github.com/nf-core/tools/pull/3191)) +- Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214)) +- Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212)) +- Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218)) + +### Linting + +- Fix bug when linting schema params and when using `defaultIgnoreParams` ([#3213](https://github.com/nf-core/tools/pull/3213)) + +### General + +- Use updated pipeline commands in docstrings ([#3215](https://github.com/nf-core/tools/pull/3215)) +- Disable automatic sync on release, fix handling empty pipeline input ([#3217](https://github.com/nf-core/tools/pull/3217)) + ## [v3.0.1 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.1) - [2024-10-09] ### Template diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index eefb59496..61738a414 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -1,5 +1,5 @@ name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors +# {% raw %}This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: push: branches: @@ -11,49 +11,75 @@ on: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: - group: "{% raw %}${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}{% endraw %}" + group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) - if: "{% raw %}${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}{% endraw %}" + if: "${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}" runs-on: ubuntu-latest strategy: matrix: NXF_VER: - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: - version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}" + version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - - name: Run pipeline with test data (docker) - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: Set up Singularity + if: matrix.profile == 'singularity' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda - - name: Run pipeline with test data (singularity) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: Set up Conda + if: matrix.profile == 'conda' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results - if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}" + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data (conda) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results - if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}" + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results{% endraw %} diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 29b994754..fdd5492ca 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -116,5 +116,4 @@ jobs: exit 1 else echo "The pipeline can be downloaded successfully!" - fi - {% endraw %}{% endif %} + fi{% endraw %}{% endif %} diff --git a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml index 58db2eb63..87a218446 100644 --- a/nf_core/pipeline-template/.github/workflows/template_version_comment.yml +++ b/nf_core/pipeline-template/.github/workflows/template_version_comment.yml @@ -10,9 +10,11 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: nichmor/minimal-read-yaml@v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -24,20 +26,21 @@ jobs: - name: Check nf-core outdated id: nf_core_outdated - run: pip list --outdated | grep nf-core + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 if: | - ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + contains(env.OUTPUT, 'nf-core') with: repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} allow-repeats: false message: | - ## :warning: Newer version of the nf-core template is available. - - Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - Please update your pipeline to the latest version. - - For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). #{%- endraw %} diff --git a/nf_core/pipeline-template/.gitignore b/nf_core/pipeline-template/.gitignore index 5124c9ac7..a42ce0162 100644 --- a/nf_core/pipeline-template/.gitignore +++ b/nf_core/pipeline-template/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/nf_core/pipeline-template/CITATIONS.md b/nf_core/pipeline-template/CITATIONS.md index 01e97c141..16da9a420 100644 --- a/nf_core/pipeline-template/CITATIONS.md +++ b/nf_core/pipeline-template/CITATIONS.md @@ -15,12 +15,14 @@ {% if fastqc %}- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. -> {% endif %} + +{%- endif %} {% if multiqc %}- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. -> {% endif %} + +{%- endif %} ## Software packaging/containerisation tools @@ -43,4 +45,5 @@ - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. - > {%- endif %} + + {%- endif %} diff --git a/nf_core/pipeline-template/docs/output.md b/nf_core/pipeline-template/docs/output.md index 1becf24b6..83d5d23fe 100644 --- a/nf_core/pipeline-template/docs/output.md +++ b/nf_core/pipeline-template/docs/output.md @@ -64,7 +64,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `pipeline_info/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. {%- if email %} - - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. {% endif %} + - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.{% endif %} - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - Parameters used by the pipeline run: `params.json`. diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf index 6516ebf90..6644d74a2 100644 --- a/nf_core/pipeline-template/main.nf +++ b/nf_core/pipeline-template/main.nf @@ -84,7 +84,8 @@ workflow { params.outdir, params.input ) - {% endif %} + {%- endif %} + // // WORKFLOW: Run main workflow // diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index fa4651ee1..f714eb1d9 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -13,7 +13,7 @@ }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", - "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } {%- endif %} @@ -23,12 +23,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }{% if nf_schema %}, "utils_nfschema_plugin": { diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf index 9724d2f34..cc0643e1d 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf @@ -52,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index f2bcda097..052a5d8b1 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -288,10 +288,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """{% endif %} }{% if is_nfcore %} summary { diff --git a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf index bcf2f4a9a..78fed1fcf 100644 --- a/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf @@ -51,7 +51,8 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - {% if nf_schema %} + {%- if nf_schema %} + // // Validate parameters and generate parameter summary to stdout // @@ -60,7 +61,7 @@ workflow PIPELINE_INITIALISATION { validate_params, null ) - {% endif %} + {%- endif %} // // Check config provided to the pipeline @@ -70,6 +71,7 @@ workflow PIPELINE_INITIALISATION { ) {%- if igenomes %} + // // Custom validation for pipeline parameters // @@ -123,7 +125,7 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML - {% endif %} + {%- endif %} outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output {% if adaptivecard or slackreport %}hook_url // string: hook URL for notifications{% endif %} diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a6..0fcbf7b3f 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -106,17 +106,19 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca4..5cb7bafef 100644 --- a/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/nf_core/pipeline-template/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index f878bb31a..adad7a6a0 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -65,13 +65,14 @@ workflow {{ short_name|upper }} { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - {% if nf_schema %} + {%- if nf_schema %} + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - {% endif %} + {%- endif %} {%- if citations %} ch_multiqc_custom_methods_description = params.multiqc_methods_description ? diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index 8b0edf34c..26e4d2328 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -41,7 +41,7 @@ class PipelineCreateApp(App[utils.CreateConfig]): """A Textual app to manage stopwatches.""" CSS_PATH = "create.tcss" - TITLE = "nf-core create" + TITLE = "nf-core pipelines create" SUB_TITLE = "Create a new pipeline with the nf-core pipeline template" BINDINGS = [ ("d", "toggle_dark", "Toggle dark mode"), diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index dd45621bc..6ae55501b 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -465,6 +465,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`." ) else: + schema_default = str(schema.schema_defaults[param_name]) failed.append( f"Default value from the Nextflow schema `{param} = {self._wrap_quotes(schema_default)}` not found in `nextflow.config`." ) diff --git a/nf_core/pipelines/lint/template_strings.py b/nf_core/pipelines/lint/template_strings.py index 37a1f64da..11c5e8251 100644 --- a/nf_core/pipelines/lint/template_strings.py +++ b/nf_core/pipelines/lint/template_strings.py @@ -5,7 +5,7 @@ def template_strings(self): """Check for template placeholders. - The ``nf-core create`` pipeline template uses + The ``nf-core pipelines create`` pipeline template uses `Jinja `_ behind the scenes. This lint test fails if any Jinja template variables such as diff --git a/nf_core/pipelines/schema.py b/nf_core/pipelines/schema.py index 1f0b4d5e3..127aa123d 100644 --- a/nf_core/pipelines/schema.py +++ b/nf_core/pipelines/schema.py @@ -97,11 +97,16 @@ def _update_validation_plugin_from_config(self) -> None: conf.get("validation.help.fullParameter", "helpFull"), conf.get("validation.help.showHiddenParameter", "showHidden"), ] # Help parameter should be ignored by default - ignored_params_config = conf.get("validation.defaultIgnoreParams", []) + ignored_params_config_str = conf.get("validation.defaultIgnoreParams", "") + ignored_params_config = [ + item.strip().strip("'") for item in ignored_params_config_str[1:-1].split(",") + ] # Extract list elements and remove whitespace + if len(ignored_params_config) > 0: log.debug(f"Ignoring parameters from config: {ignored_params_config}") ignored_params.extend(ignored_params_config) self.ignored_params = ignored_params + log.debug(f"Ignoring parameters: {self.ignored_params}") self.schema_draft = "https://json-schema.org/draft/2020-12/schema" else: diff --git a/setup.py b/setup.py index 364372f57..78b56fe38 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.0.1" +version = "3.0.2" with open("README.md") as f: readme = f.read() diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index 5c4a15831..0e1682290 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-1899994154-matrix { + .terminal-1305977867-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1899994154-title { + .terminal-1305977867-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1899994154-r1 { fill: #c5c8c6 } -.terminal-1899994154-r2 { fill: #e3e3e3 } -.terminal-1899994154-r3 { fill: #989898 } -.terminal-1899994154-r4 { fill: #e1e1e1 } -.terminal-1899994154-r5 { fill: #4ebf71;font-weight: bold } -.terminal-1899994154-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-1899994154-r7 { fill: #1e1e1e } -.terminal-1899994154-r8 { fill: #008139 } -.terminal-1899994154-r9 { fill: #121212 } -.terminal-1899994154-r10 { fill: #e2e2e2 } -.terminal-1899994154-r11 { fill: #787878 } -.terminal-1899994154-r12 { fill: #454a50 } -.terminal-1899994154-r13 { fill: #7ae998 } -.terminal-1899994154-r14 { fill: #e2e3e3;font-weight: bold } -.terminal-1899994154-r15 { fill: #0a180e;font-weight: bold } -.terminal-1899994154-r16 { fill: #000000 } -.terminal-1899994154-r17 { fill: #fea62b;font-weight: bold } -.terminal-1899994154-r18 { fill: #a7a9ab } -.terminal-1899994154-r19 { fill: #e2e3e3 } + .terminal-1305977867-r1 { fill: #c5c8c6 } +.terminal-1305977867-r2 { fill: #e3e3e3 } +.terminal-1305977867-r3 { fill: #989898 } +.terminal-1305977867-r4 { fill: #e1e1e1 } +.terminal-1305977867-r5 { fill: #4ebf71;font-weight: bold } +.terminal-1305977867-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-1305977867-r7 { fill: #1e1e1e } +.terminal-1305977867-r8 { fill: #008139 } +.terminal-1305977867-r9 { fill: #121212 } +.terminal-1305977867-r10 { fill: #e2e2e2 } +.terminal-1305977867-r11 { fill: #787878 } +.terminal-1305977867-r12 { fill: #454a50 } +.terminal-1305977867-r13 { fill: #7ae998 } +.terminal-1305977867-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-1305977867-r15 { fill: #0a180e;font-weight: bold } +.terminal-1305977867-r16 { fill: #000000 } +.terminal-1305977867-r17 { fill: #fea62b;font-weight: bold } +.terminal-1305977867-r18 { fill: #a7a9ab } +.terminal-1305977867-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index 4445dc68a..02f4fc213 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,256 +19,256 @@ font-weight: 700; } - .terminal-3411435506-matrix { + .terminal-667641811-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3411435506-title { + .terminal-667641811-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3411435506-r1 { fill: #c5c8c6 } -.terminal-3411435506-r2 { fill: #e3e3e3 } -.terminal-3411435506-r3 { fill: #989898 } -.terminal-3411435506-r4 { fill: #e1e1e1 } -.terminal-3411435506-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3411435506-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-3411435506-r7 { fill: #1e1e1e } -.terminal-3411435506-r8 { fill: #0f4e2a } -.terminal-3411435506-r9 { fill: #0178d4 } -.terminal-3411435506-r10 { fill: #a7a7a7 } -.terminal-3411435506-r11 { fill: #787878 } -.terminal-3411435506-r12 { fill: #e2e2e2 } -.terminal-3411435506-r13 { fill: #121212 } -.terminal-3411435506-r14 { fill: #454a50 } -.terminal-3411435506-r15 { fill: #7ae998 } -.terminal-3411435506-r16 { fill: #e2e3e3;font-weight: bold } -.terminal-3411435506-r17 { fill: #0a180e;font-weight: bold } -.terminal-3411435506-r18 { fill: #000000 } -.terminal-3411435506-r19 { fill: #008139 } -.terminal-3411435506-r20 { fill: #fea62b;font-weight: bold } -.terminal-3411435506-r21 { fill: #a7a9ab } -.terminal-3411435506-r22 { fill: #e2e3e3 } + .terminal-667641811-r1 { fill: #c5c8c6 } +.terminal-667641811-r2 { fill: #e3e3e3 } +.terminal-667641811-r3 { fill: #989898 } +.terminal-667641811-r4 { fill: #e1e1e1 } +.terminal-667641811-r5 { fill: #4ebf71;font-weight: bold } +.terminal-667641811-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-667641811-r7 { fill: #1e1e1e } +.terminal-667641811-r8 { fill: #0f4e2a } +.terminal-667641811-r9 { fill: #0178d4 } +.terminal-667641811-r10 { fill: #a7a7a7 } +.terminal-667641811-r11 { fill: #787878 } +.terminal-667641811-r12 { fill: #e2e2e2 } +.terminal-667641811-r13 { fill: #121212 } +.terminal-667641811-r14 { fill: #454a50 } +.terminal-667641811-r15 { fill: #7ae998 } +.terminal-667641811-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-667641811-r17 { fill: #0a180e;font-weight: bold } +.terminal-667641811-r18 { fill: #000000 } +.terminal-667641811-r19 { fill: #008139 } +.terminal-667641811-r20 { fill: #fea62b;font-weight: bold } +.terminal-667641811-r21 { fill: #a7a9ab } +.terminal-667641811-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index f32d5271e..73ba989e0 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the ● Your pipeline will never be part of  -nf-core communitynf-core -● You think that there's an outside chance ● You want full control over all features  -that it ever could be part of nf-corethat are included from the template  -(including those that are mandatory for  -nf-core). -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -  Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the ● Your pipeline will never be part of  +nf-core communitynf-core +● You think that there's an outside chance ● You want full control over all features  +that it ever could be part of nf-corethat are included from the template  +(including those that are mandatory for  +nf-core). +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +  Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index 8969694cb..d469a4761 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,257 +19,257 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Template features - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use a GitHub Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing▄▄ - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use reference genomesThe pipeline will be  Hide help  -▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - - -Nf-core pipelines are configured to use a copy of the most common reference  -genome files. - -By selecting this option, your pipeline will include a configuration file  -specifying the paths to these files. - -The required code to use these files will also be included in the template.  -When the pipeline user provides an appropriate genome key, the pipeline will -automatically download the required reference files. -▅▅ -For more information about reference genomes in nf-core pipelines, see the  - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing▄▄ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Hide help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + + +Nf-core pipelines are configured to use a copy of the most common reference  +genome files. + +By selecting this option, your pipeline will include a configuration file  +specifying the paths to these files. + +The required code to use these files will also be included in the template.  +When the pipeline user provides an appropriate genome key, the pipeline will +automatically download the required reference files. +▅▅ +For more information about reference genomes in nf-core pipelines, see the  + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index ddd0ff57e..b34483176 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,251 +19,251 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Final details - - - - -First version of the pipelinePath to the output directory where the  -pipeline will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊1.0.0dev▎▊.                                         ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Final details + + + + +First version of the pipelinePath to the output directory where the  +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 3013b9961..9276d5348 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,258 +19,258 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Create GitHub repository - -  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    -  the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -The name of the organisation where the The name of the new GitHub repository -GitHub repo will be cretaed -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user  -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Create GitHub repository + +  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    +  the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +The name of the organisation where the The name of the new GitHub repository +GitHub repo will be cretaed +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user  +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg index 3612a062c..f840f8849 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -19,254 +19,254 @@ font-weight: 700; } - .terminal-1078212293-matrix { + .terminal-1075265190-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1078212293-title { + .terminal-1075265190-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1078212293-r1 { fill: #c5c8c6 } -.terminal-1078212293-r2 { fill: #e3e3e3 } -.terminal-1078212293-r3 { fill: #989898 } -.terminal-1078212293-r4 { fill: #e1e1e1 } -.terminal-1078212293-r5 { fill: #4ebf71;font-weight: bold } -.terminal-1078212293-r6 { fill: #98e024 } -.terminal-1078212293-r7 { fill: #626262 } -.terminal-1078212293-r8 { fill: #9d65ff } -.terminal-1078212293-r9 { fill: #fd971f } -.terminal-1078212293-r10 { fill: #d2d2d2 } -.terminal-1078212293-r11 { fill: #82aaff } -.terminal-1078212293-r12 { fill: #eeffff } -.terminal-1078212293-r13 { fill: #18954b } -.terminal-1078212293-r14 { fill: #e2e2e2 } -.terminal-1078212293-r15 { fill: #969696;font-weight: bold } -.terminal-1078212293-r16 { fill: #7ae998 } -.terminal-1078212293-r17 { fill: #008139 } -.terminal-1078212293-r18 { fill: #fea62b;font-weight: bold } -.terminal-1078212293-r19 { fill: #a7a9ab } -.terminal-1078212293-r20 { fill: #e2e3e3 } + .terminal-1075265190-r1 { fill: #c5c8c6 } +.terminal-1075265190-r2 { fill: #e3e3e3 } +.terminal-1075265190-r3 { fill: #989898 } +.terminal-1075265190-r4 { fill: #e1e1e1 } +.terminal-1075265190-r5 { fill: #4ebf71;font-weight: bold } +.terminal-1075265190-r6 { fill: #98e024 } +.terminal-1075265190-r7 { fill: #626262 } +.terminal-1075265190-r8 { fill: #9d65ff } +.terminal-1075265190-r9 { fill: #fd971f } +.terminal-1075265190-r10 { fill: #d2d2d2 } +.terminal-1075265190-r11 { fill: #82aaff } +.terminal-1075265190-r12 { fill: #eeffff } +.terminal-1075265190-r13 { fill: #18954b } +.terminal-1075265190-r14 { fill: #e2e2e2 } +.terminal-1075265190-r15 { fill: #969696;font-weight: bold } +.terminal-1075265190-r16 { fill: #7ae998 } +.terminal-1075265190-r17 { fill: #008139 } +.terminal-1075265190-r18 { fill: #fea62b;font-weight: bold } +.terminal-1075265190-r19 { fill: #a7a9ab } +.terminal-1075265190-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -  If you would like to create the GitHub repository later, you can do it manually by following  -  these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +  If you would like to create the GitHub repository later, you can do it manually by following  +  these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index a0ca3d70d..f302feaae 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -19,247 +19,247 @@ font-weight: 700; } - .terminal-2285979206-matrix { + .terminal-3993718311-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2285979206-title { + .terminal-3993718311-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2285979206-r1 { fill: #c5c8c6 } -.terminal-2285979206-r2 { fill: #e3e3e3 } -.terminal-2285979206-r3 { fill: #989898 } -.terminal-2285979206-r4 { fill: #e1e1e1 } -.terminal-2285979206-r5 { fill: #4ebf71;font-weight: bold } -.terminal-2285979206-r6 { fill: #7ae998 } -.terminal-2285979206-r7 { fill: #507bb3 } -.terminal-2285979206-r8 { fill: #dde6ed;font-weight: bold } -.terminal-2285979206-r9 { fill: #008139 } -.terminal-2285979206-r10 { fill: #001541 } -.terminal-2285979206-r11 { fill: #fea62b;font-weight: bold } -.terminal-2285979206-r12 { fill: #a7a9ab } -.terminal-2285979206-r13 { fill: #e2e3e3 } + .terminal-3993718311-r1 { fill: #c5c8c6 } +.terminal-3993718311-r2 { fill: #e3e3e3 } +.terminal-3993718311-r3 { fill: #989898 } +.terminal-3993718311-r4 { fill: #e1e1e1 } +.terminal-3993718311-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3993718311-r6 { fill: #7ae998 } +.terminal-3993718311-r7 { fill: #507bb3 } +.terminal-3993718311-r8 { fill: #dde6ed;font-weight: bold } +.terminal-3993718311-r9 { fill: #008139 } +.terminal-3993718311-r10 { fill: #001541 } +.terminal-3993718311-r11 { fill: #fea62b;font-weight: bold } +.terminal-3993718311-r12 { fill: #a7a9ab } +.terminal-3993718311-r13 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Create GitHub repository - - -  After creating the pipeline template locally, we can create a GitHub repository and push the  -  code to it. - -  Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Create GitHub repository + + +  After creating the pipeline template locally, we can create a GitHub repository and push the  +  code to it. + +  Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index 7ff071efa..399989e47 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,255 +19,255 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Template features - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use a GitHub Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing -▃▃ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add configuration The pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -profiles containing  -custom parameters  -requried to run  -nf-core pipelines at  -different institutions - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use code lintersThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -and CI tests to lint  -your code: pre-commit, -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing +▃▃ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add configuration The pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +profiles containing  +custom parameters  +requried to run  +nf-core pipelines at  +different institutions + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use code lintersThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +and CI tests to lint  +your code: pre-commit, +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index 48b9b91e9..eae763718 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,254 +19,254 @@ font-weight: 700; } - .terminal-3384959394-matrix { + .terminal-3985795459-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3384959394-title { + .terminal-3985795459-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3384959394-r1 { fill: #c5c8c6 } -.terminal-3384959394-r2 { fill: #e3e3e3 } -.terminal-3384959394-r3 { fill: #989898 } -.terminal-3384959394-r4 { fill: #e1e1e1 } -.terminal-3384959394-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3384959394-r6 { fill: #1e1e1e } -.terminal-3384959394-r7 { fill: #507bb3 } -.terminal-3384959394-r8 { fill: #e2e2e2 } -.terminal-3384959394-r9 { fill: #808080 } -.terminal-3384959394-r10 { fill: #dde6ed;font-weight: bold } -.terminal-3384959394-r11 { fill: #001541 } -.terminal-3384959394-r12 { fill: #454a50 } -.terminal-3384959394-r13 { fill: #7ae998 } -.terminal-3384959394-r14 { fill: #e2e3e3;font-weight: bold } -.terminal-3384959394-r15 { fill: #0a180e;font-weight: bold } -.terminal-3384959394-r16 { fill: #000000 } -.terminal-3384959394-r17 { fill: #008139 } -.terminal-3384959394-r18 { fill: #fea62b;font-weight: bold } -.terminal-3384959394-r19 { fill: #a7a9ab } -.terminal-3384959394-r20 { fill: #e2e3e3 } + .terminal-3985795459-r1 { fill: #c5c8c6 } +.terminal-3985795459-r2 { fill: #e3e3e3 } +.terminal-3985795459-r3 { fill: #989898 } +.terminal-3985795459-r4 { fill: #e1e1e1 } +.terminal-3985795459-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3985795459-r6 { fill: #1e1e1e } +.terminal-3985795459-r7 { fill: #507bb3 } +.terminal-3985795459-r8 { fill: #e2e2e2 } +.terminal-3985795459-r9 { fill: #808080 } +.terminal-3985795459-r10 { fill: #dde6ed;font-weight: bold } +.terminal-3985795459-r11 { fill: #001541 } +.terminal-3985795459-r12 { fill: #454a50 } +.terminal-3985795459-r13 { fill: #7ae998 } +.terminal-3985795459-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-3985795459-r15 { fill: #0a180e;font-weight: bold } +.terminal-3985795459-r16 { fill: #000000 } +.terminal-3985795459-r17 { fill: #008139 } +.terminal-3985795459-r18 { fill: #fea62b;font-weight: bold } +.terminal-3985795459-r19 { fill: #a7a9ab } +.terminal-3985795459-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Template features - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most common -reference genome files  -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use multiqcThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which generates  -an HTML report for  -quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use fastqcThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which performs  -quality control  -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use nf-schemaUse the nf-schema  Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -this pipeline. - - - - - - - - - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most common +reference genome files  +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use multiqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which generates  +an HTML report for  +quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use fastqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which performs  +quality control  +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use nf-schemaUse the nf-schema  Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +this pipeline. + + + + + + + + + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index 7e55b2b0f..2253bd9ab 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-2071915686-matrix { + .terminal-3773691015-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2071915686-title { + .terminal-3773691015-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2071915686-r1 { fill: #c5c8c6 } -.terminal-2071915686-r2 { fill: #e3e3e3 } -.terminal-2071915686-r3 { fill: #989898 } -.terminal-2071915686-r4 { fill: #e1e1e1 } -.terminal-2071915686-r5 { fill: #4ebf71;font-weight: bold } -.terminal-2071915686-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-2071915686-r7 { fill: #1e1e1e } -.terminal-2071915686-r8 { fill: #0f4e2a } -.terminal-2071915686-r9 { fill: #7b3042 } -.terminal-2071915686-r10 { fill: #a7a7a7 } -.terminal-2071915686-r11 { fill: #787878 } -.terminal-2071915686-r12 { fill: #e2e2e2 } -.terminal-2071915686-r13 { fill: #b93c5b } -.terminal-2071915686-r14 { fill: #454a50 } -.terminal-2071915686-r15 { fill: #7ae998 } -.terminal-2071915686-r16 { fill: #e2e3e3;font-weight: bold } -.terminal-2071915686-r17 { fill: #000000 } -.terminal-2071915686-r18 { fill: #008139 } -.terminal-2071915686-r19 { fill: #fea62b;font-weight: bold } -.terminal-2071915686-r20 { fill: #a7a9ab } -.terminal-2071915686-r21 { fill: #e2e3e3 } + .terminal-3773691015-r1 { fill: #c5c8c6 } +.terminal-3773691015-r2 { fill: #e3e3e3 } +.terminal-3773691015-r3 { fill: #989898 } +.terminal-3773691015-r4 { fill: #e1e1e1 } +.terminal-3773691015-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3773691015-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-3773691015-r7 { fill: #1e1e1e } +.terminal-3773691015-r8 { fill: #0f4e2a } +.terminal-3773691015-r9 { fill: #7b3042 } +.terminal-3773691015-r10 { fill: #a7a7a7 } +.terminal-3773691015-r11 { fill: #787878 } +.terminal-3773691015-r12 { fill: #e2e2e2 } +.terminal-3773691015-r13 { fill: #b93c5b } +.terminal-3773691015-r14 { fill: #454a50 } +.terminal-3773691015-r15 { fill: #7ae998 } +.terminal-3773691015-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-3773691015-r17 { fill: #000000 } +.terminal-3773691015-r18 { fill: #008139 } +.terminal-3773691015-r19 { fill: #fea62b;font-weight: bold } +.terminal-3773691015-r20 { fill: #a7a9ab } +.terminal-3773691015-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index 2670307c2..af00bd0b7 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-3972722241-matrix { + .terminal-3664377378-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3972722241-title { + .terminal-3664377378-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3972722241-r1 { fill: #c5c8c6 } -.terminal-3972722241-r2 { fill: #e3e3e3 } -.terminal-3972722241-r3 { fill: #989898 } -.terminal-3972722241-r4 { fill: #98e024 } -.terminal-3972722241-r5 { fill: #626262 } -.terminal-3972722241-r6 { fill: #9d65ff } -.terminal-3972722241-r7 { fill: #fd971f } -.terminal-3972722241-r8 { fill: #e1e1e1 } -.terminal-3972722241-r9 { fill: #4ebf71;font-weight: bold } -.terminal-3972722241-r10 { fill: #e1e1e1;text-decoration: underline; } -.terminal-3972722241-r11 { fill: #18954b } -.terminal-3972722241-r12 { fill: #e2e2e2 } -.terminal-3972722241-r13 { fill: #e2e2e2;text-decoration: underline; } -.terminal-3972722241-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; } -.terminal-3972722241-r15 { fill: #7ae998 } -.terminal-3972722241-r16 { fill: #008139 } -.terminal-3972722241-r17 { fill: #fea62b;font-weight: bold } -.terminal-3972722241-r18 { fill: #a7a9ab } -.terminal-3972722241-r19 { fill: #e2e3e3 } + .terminal-3664377378-r1 { fill: #c5c8c6 } +.terminal-3664377378-r2 { fill: #e3e3e3 } +.terminal-3664377378-r3 { fill: #989898 } +.terminal-3664377378-r4 { fill: #98e024 } +.terminal-3664377378-r5 { fill: #626262 } +.terminal-3664377378-r6 { fill: #9d65ff } +.terminal-3664377378-r7 { fill: #fd971f } +.terminal-3664377378-r8 { fill: #e1e1e1 } +.terminal-3664377378-r9 { fill: #4ebf71;font-weight: bold } +.terminal-3664377378-r10 { fill: #e1e1e1;text-decoration: underline; } +.terminal-3664377378-r11 { fill: #18954b } +.terminal-3664377378-r12 { fill: #e2e2e2 } +.terminal-3664377378-r13 { fill: #e2e2e2;text-decoration: underline; } +.terminal-3664377378-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; } +.terminal-3664377378-r15 { fill: #7ae998 } +.terminal-3664377378-r16 { fill: #008139 } +.terminal-3664377378-r17 { fill: #fea62b;font-weight: bold } +.terminal-3664377378-r18 { fill: #a7a9ab } +.terminal-3664377378-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core create + nf-core pipelines create - - - - ⭘nf-core create — Create a new pipeline with the nf-core pipeline template - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    -  pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the  -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    +  pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the  +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit