diff --git a/.gitattributes b/.gitattributes index c1c17000..7a2dabc2 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,5 +1,4 @@ *.config linguist-language=nextflow *.nf.test linguist-language=nextflow -tests/**/*nf.test.snap linguist-generated modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 69af505f..d8a12ddd 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 9a85c826..2044959f 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7b7070e7..566ef509 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,67 +1,28 @@ -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: pull_request: release: types: [published] - merge_group: - types: - - checks_requested - branches: - - master - - dev - - refactor env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.0-rc1" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: - changes: - name: Check for changes - runs-on: ubuntu-latest - outputs: - # Expose matched filters as job 'tags' output variable - tags: ${{ steps.filter.outputs.changes }} - steps: - - uses: actions/checkout@v3 - - uses: dorny/paths-filter@v2 - id: filter - with: - filters: ".github/tags.yml" - - define_nxf_versions: - name: Choose nextflow versions to test against depending on target branch - runs-on: ubuntu-latest - outputs: - matrix: ${{ steps.nxf_versions.outputs.matrix }} - steps: - - id: nxf_versions - run: | - if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then - echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT - else - echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT - fi - test: - name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} - needs: [changes, define_nxf_versions] - if: needs.changes.outputs.tags != '[]' + name: Run pipeline with test data + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}" runs-on: ubuntu-latest strategy: - fail-fast: false matrix: - NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} - tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] - profile: - - "docker" - + NXF_VER: + - "23.04.0" + - "latest-everything" steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -71,23 +32,29 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Install nf-test + - name: Run pipeline with test data run: | - wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER - sudo mv nf-test /usr/local/bin/ + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results - - name: Run nf-test - run: | - nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml + parameters: + name: Test workflow parameters + if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }} + runs-on: ubuntu-latest + strategy: + matrix: + parameters: + - "--nf_core_pipeline rnaseq" + - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout" + - "--skip_fastq_download" + - "--force_sratools_download" + steps: + - name: Check out pipeline code + uses: actions/checkout@v2 - - name: Output log on failure - if: failure() + - name: Install Nextflow run: | - sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log - - - name: Publish Test Report - uses: mikepenz/action-junit-report@v3 - if: always() # always run even if the previous step fails - with: - report_paths: test.xml + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + - name: Run pipeline with various parameters + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} diff --git a/.gitignore b/.gitignore index b1b5890a..5124c9ac 100644 --- a/.gitignore +++ b/.gitignore @@ -6,6 +6,3 @@ results/ testing/ testing* *.pyc -.nf-test/ -nf-test -.nf-test.log diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index 269ee3ed..9975ac5b 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -4,14 +4,5 @@ lint: files_exist: - conf/modules.config files_unchanged: - - .github/CONTRIBUTING.md - - .github/ISSUE_TEMPLATE/bug_report.yml - - assets/nf-core-fetchngs_logo_light.png - assets/sendmail_template.txt - lib/NfcoreTemplate.groovy - - .gitattributes - multiqc_config: false - nextflow_config: - - "params.validationShowHiddenParams" - - "params.validationSchemaIgnoreParams" - schema_params: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 92e31da4..daf474c0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,23 +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). -## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-06-29 - -### Credits - -Special thanks to the following for their contributions to the release: - -- [Sateesh Peri](https://github.com/sateeshperi) -- [Edmund Miller](https://github.com/Emiller88) -- [Maxime Garcia](https://github.com/maxulysse) - -Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. - -### Enhancements & fixes - -- [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests -- [#184](https://github.com/nf-core/fetchngs/pull/184) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow) -- [#195](https://github.com/nf-core/fetchngs/pull/195) Separate configuration files for all modules +## dev - [date] ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 diff --git a/CITATIONS.md b/CITATIONS.md index 3826bfe7..4b641f6c 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -57,5 +57,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [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. diff --git a/README.md b/README.md index 4d6c2d35..7b2c1ed1 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![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/) @@ -50,7 +50,7 @@ nextflow run nf-core/fetchngs \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/fetchngs/usage) and the [parameter documentation](https://nf-co.re/fetchngs/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/fetchngs/usage) and the [parameter documentation](https://nf-co.re/fetchngs/parameters). ## Supported ids diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index f9309867..49a0a9fd 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/fetchngs Methods Description" section_href: "https://github.com/nf-core/fetchngs" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/fetchngs v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/fetchngs v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
+

${tool_citations}

References

Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index a7d7cf37..5e3d9889 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/fetchngs + This report has been generated by the nf-core/fetchngs analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-fetchngs-methods-description": order: -1000 diff --git a/assets/nf-core-fetchngs_logo_light.png b/assets/nf-core-fetchngs_logo_light.png index 08c7d855..c201c150 100644 Binary files a/assets/nf-core-fetchngs_logo_light.png and b/assets/nf-core-fetchngs_logo_light.png differ diff --git a/assets/schema_input.json b/assets/schema_input.json index 9a800216..d451f9e9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -5,11 +5,13 @@ "description": "Schema for the file provided with params.input", "type": "array", "items": { - "type": "array", - "items": { - "type": "string", - "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$", - "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier" + "type": "object", + "properties": { + "id": { + "type": "string", + "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$", + "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier" + } } } } diff --git a/assets/slackreport.json b/assets/slackreport.json index 043d02f2..aa5db2a1 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_name": "nf-core/fetchngs v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/bin/sra_runinfo_to_ftp.py b/bin/sra_runinfo_to_ftp.py index c220f74e..ef80ec80 100755 --- a/bin/sra_runinfo_to_ftp.py +++ b/bin/sra_runinfo_to_ftp.py @@ -61,8 +61,7 @@ def parse_sra_runinfo(file_in): with open(file_in, "r", newline="") as fin: reader = csv.DictReader(fin, delimiter="\t", skipinitialspace=True) header = list(reader.fieldnames) - missing = frozenset(columns).difference(frozenset(header)) - if missing: + if missing := frozenset(columns).difference(frozenset(header)): logger.critical(f"The following expected columns are missing from {file_in}: " f"{', '.join(missing)}.") sys.exit(1) for row in reader: diff --git a/conf/test.config b/conf/test.config index 6a9d5d38..3c58e9cf 100644 --- a/conf/test.config +++ b/conf/test.config @@ -21,6 +21,4 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' - - schema_ignore_params = 'fastq_ftp_ids,genomes,merge_samplesheet_ids,test_data,test_data_base' } diff --git a/conf/test_data.config b/conf/test_data.config deleted file mode 100644 index 42d3d818..00000000 --- a/conf/test_data.config +++ /dev/null @@ -1,36 +0,0 @@ -params { - // Base directory for test data - test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs" - - merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ] - - def merge_samplesheet_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/" - def merge_mappings_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/" - def merge_samplesheet_urls = [] - def merge_mappings_urls = [] - - merge_samplesheet_ids.each { id -> - merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv" - merge_mappings_urls += "${merge_mappings_url}/${id}.mappings.csv" - } - - fastq_ftp_ids = ["SRR13191702"] - def fastq_ftp_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/" - def fastq_ftp_urls = [] - - fastq_ftp_ids.each { id -> - fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz" - fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz" - } - - test_data { - 'modules_local' { - multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv" - sra_merge_samplesheet_samplesheets = merge_samplesheet_urls - sra_merge_samplesheet_mappings = merge_mappings_urls - sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv" - sra_fastq_ftp = fastq_ftp_urls - sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv" - } - } -} diff --git a/conf/test_full.config b/conf/test_full.config index fed693e0..c16fda7f 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index b2cd7b50..0720a680 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -70,12 +70,6 @@ From v1.9 of this pipeline the default `strandedness` in the output samplesheet If FTP connections are blocked on your network use the [`--force_sratools_download`](https://nf-co.re/fetchngs/parameters#force_sratools_download) parameter to force the pipeline to download data using sra-tools instead of the ENA FTP. -### Downloading 10X Genomics Data - -As of v1.10.0, this pipeline now supports downloading of 10X Genomics data. For 10X data sets, the output needs to be split into three fastq files, consisting of the feature barcode+UMI, cDNA sequence reads, and sample index. Adding the `--force_sratools_download` parameter will cause the pipeline to use the sra-tools fasterq-dump program with appropriate setting to ensure that all three files are generated. - -Please note that in our experience the downloaded R1, R2, and R3 fastq files do not always correspond to the same data types across different submissions. In many cases, R1 will be the cell barcode + UMI, R2 is the cDNA sequence, and R3 is the sample index. However, this is not alway the case. Users are strongly encouraged to verify their data before proceeding with downstream analysis. - ### Downloading dbGAP data with JWT As of v1.10.0, the SRA Toolkit used in this pipeline can be configured to access protected data from dbGAP using a [JWT cart file](https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbGAP-cloud-download/) on a supported cloud computing environment (Amazon Web Services or Google Cloud Platform). The JWT cart file can be specified with `--dbgap_key /path/to/cart.jwt`. diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NftestUtils.groovy b/lib/NftestUtils.groovy deleted file mode 100644 index ce6fc8b4..00000000 --- a/lib/NftestUtils.groovy +++ /dev/null @@ -1,38 +0,0 @@ -// Helper functions for pipeline tests - -class NftestUtils { - - // Function to remove Nextflow version from software_versions.yml - public static String removeNextflowVersion(outputDir) { - def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml - if (softwareVersions.containsKey("Workflow")) { - softwareVersions.Workflow.remove("Nextflow") - } - return softwareVersions - } - - // Function to filter lines from a file and return a new file - public static File filterLines(String inFilePath, int linesToSkip) { - if (linesToSkip >= 0) { - File inputFile = new File(inFilePath) - File outputFile = new File(inFilePath + ".filtered") - def lineCount = 0 - inputFile.eachLine { line -> - lineCount++ - if (lineCount > linesToSkip) { - outputFile.append(line + '\n') - } - } - return outputFile - } else { - File inputFile = new File(inFilePath) - File outputFile = new File(inFilePath + ".filtered") - def lines = inputFile.readLines() - def totalLines = lines.size() - lines.take(totalLines + linesToSkip).each { line -> - outputFile.append(line + '\n') - } - return outputFile - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 99858d2a..f9469941 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -19,42 +19,12 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input ids.csv -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } - // Print workflow version and exit on --version if (params.version) { String workflow_version = NfcoreTemplate.version(workflow) @@ -62,14 +32,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/main.nf b/main.nf index 0535bb57..355898d0 100644 --- a/main.nf +++ b/main.nf @@ -17,7 +17,25 @@ nextflow.enable.dsl = 2 ======================================================================================== */ -WorkflowMain.initialise(workflow, params, log) +include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation' + +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation + +// Print help message if needed +if (params.help) { + def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} // Check if --input file is empty ch_input = file(params.input, checkIfExists: true) @@ -47,16 +65,12 @@ if (params.input_type == 'sra') { ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5'] ] - def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) - // Validate input parameters WorkflowSra.initialise(params, valid_params) } if (params.input_type == 'synapse') { - def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) - // Create channel for synapse config if (params.synapse_config) { ch_synapse_config = file(params.synapse_config, checkIfExists: true) diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test deleted file mode 100644 index 3bf79537..00000000 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test +++ /dev/null @@ -1,31 +0,0 @@ -nextflow_process { - - name "Test process: MULTIQC_MAPPINGS_CONFIG" - script "modules/local/multiqc_mappings_config/main.nf" - process "MULTIQC_MAPPINGS_CONFIG" - tag "modules" - tag "modules_local" - tag "multiqc_mappings_config" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap b/modules/local/multiqc_mappings_config/tests/main.nf.test.snap deleted file mode 100644 index 9cf7fb38..00000000 --- a/modules/local/multiqc_mappings_config/tests/main.nf.test.snap +++ /dev/null @@ -1,52 +0,0 @@ -{ - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ], - "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ] - } - ], - "timestamp": "2023-08-17T12:02:35+0000" - }, - "Should run without failures": { - "content": [ - { - "0": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ], - "1": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "versions": [ - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ], - "yml": [ - [ - "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a", - "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73" - ] - ] - } - ], - "timestamp": "2023-08-17T12:02:35+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test deleted file mode 100644 index 7892d156..00000000 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test +++ /dev/null @@ -1,34 +0,0 @@ -nextflow_process { - - name "Test process: SRA_FASTQ_FTP" - script "modules/local/sra_fastq_ftp/main.nf" - process "SRA_FASTQ_FTP" - tag "modules" - tag "modules_local" - tag "sra_fastq_ftp" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = [ - [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map - params.test_data['modules_local']['sra_fastq_ftp'] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap b/modules/local/sra_fastq_ftp/tests/main.nf.test.snap deleted file mode 100644 index c0d5ffdc..00000000 --- a/modules/local/sra_fastq_ftp/tests/main.nf.test.snap +++ /dev/null @@ -1,140 +0,0 @@ -{ - "SRX9626017_SRR13191702": { - "content": [ - { - "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "2": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ], - "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "versions": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ] - } - ], - "timestamp": "2023-08-06T23:31:57+0000" - }, - "Should run without failures": { - "content": [ - { - "0": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "1": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "2": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ], - "fastq": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "md5": [ - [ - { - "id": "SRX9626017_SRR13191702", - "single_end": false, - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98" - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ] - ], - "versions": [ - "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b" - ] - } - ], - "timestamp": "2023-08-06T23:31:57+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test deleted file mode 100644 index f8a44086..00000000 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test +++ /dev/null @@ -1,32 +0,0 @@ -nextflow_process { - - name "Test process: SRA_IDS_TO_RUNINFO" - script "modules/local/sra_ids_to_runinfo/main.nf" - process "SRA_IDS_TO_RUNINFO" - tag "modules" - tag "modules_local" - tag "sra_ids_to_runinfo" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = 'SRR13191702' - input[1] = '' - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap b/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap deleted file mode 100644 index dbca931f..00000000 --- a/modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap +++ /dev/null @@ -1,21 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" - ], - "1": [ - "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" - ], - "tsv": [ - "SRR13191702.runinfo.tsv:md5,3a1be35781ca6e8a28d8fd4d2f3bbe85" - ], - "versions": [ - "versions.yml:md5,1c14442e9b494b586eafe41e77300fae" - ] - } - ], - "timestamp": "2023-08-06T23:30:51+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test deleted file mode 100644 index e37039bd..00000000 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test +++ /dev/null @@ -1,32 +0,0 @@ -nextflow_process { - - name "Test process: SRA_MERGE_SAMPLESHEET" - script "modules/local/sra_merge_samplesheet/main.nf" - process "SRA_MERGE_SAMPLESHEET" - tag "modules" - tag "modules_local" - tag "sra_merge_samplesheet" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = params.test_data['modules_local']['sra_merge_samplesheet_samplesheets'].collect { file(it, checkIfExists: true) } - input[1] = params.test_data['modules_local']['sra_merge_samplesheet_mappings'].collect { file(it, checkIfExists: true) } - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap deleted file mode 100644 index c5f06aac..00000000 --- a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" - ], - "1": [ - "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" - ], - "2": [ - "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" - ], - "mappings": [ - "id_mappings.csv:md5,07262807636ce4b50102308eabdcf253" - ], - "samplesheet": [ - "samplesheet.csv:md5,ef756557b0735becd2574c2a3f5840b2" - ], - "versions": [ - "versions.yml:md5,410006679d5e496d8c55e58e78ca6b34" - ] - } - ], - "timestamp": "2023-07-06T13:16:36+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test deleted file mode 100644 index 1558ff39..00000000 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test +++ /dev/null @@ -1,31 +0,0 @@ -nextflow_process { - - name "Test process: SRA_RUNINFO_TO_FTP" - script "modules/local/sra_runinfo_to_ftp/main.nf" - process "SRA_RUNINFO_TO_FTP" - tag "modules" - tag "modules_local" - tag "sra_runinfo_to_ftp" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = file(params.test_data['modules_local']['sra_runinfo_to_ftp'], checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap deleted file mode 100644 index 71a25f99..00000000 --- a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap +++ /dev/null @@ -1,21 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" - ], - "1": [ - "versions.yml:md5,e95f8185f665127a73622a19d321bcca" - ], - "tsv": [ - "SRR13191702.runinfo_ftp.tsv:md5,94378c448c044b3e20e5c54e442ab62e" - ], - "versions": [ - "versions.yml:md5,e95f8185f665127a73622a19d321bcca" - ] - } - ], - "timestamp": "2023-08-06T23:13:20+0000" - } -} \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test deleted file mode 100644 index b2ec5b11..00000000 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test +++ /dev/null @@ -1,34 +0,0 @@ -nextflow_process { - - name "Test process: SRA_TO_SAMPLESHEET" - script "modules/local/sra_to_samplesheet/main.nf" - process "SRA_TO_SAMPLESHEET" - tag "modules" - tag "modules_local" - tag "sra_to_samplesheet" - - test("Should run without failures") { - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = [id:'ERX1188904_ERR1109373', run_accession:'ERR1109373', experiment_accession:'ERX1188904', sample_accession:'SAMEA3643867', experiment_alias:'ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7', run_alias:'ena-RUN-CAM-03-11-2015-17:01:52:847-7', sample_alias:'sample_56', study_alias:'ena-STUDY-CAM-02-11-2015-17:42:24:189-13', library_layout:'PAIRED', experiment_title:'Illumina HiSeq 2500 paired end sequencing', sample_title:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', sample_description:'RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome', fastq_md5:'8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9', fastq_ftp:'ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz', fastq_1:'./results/fastq/ERX1188904_ERR1109373_1.fastq.gz', fastq_2:'./results/fastq/ERX1188904_ERR1109373_2.fastq.gz', md5_1:'9fd57225d6c07a31843276d6df9b15c0', md5_2:'5a62e8f785687dce890cfb4fe3e607f9', single_end:false] - input[1] = 'rnaseq' - input[2] = 'auto' - input[3] = 'experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description' - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap b/modules/local/sra_to_samplesheet/tests/main.nf.test.snap deleted file mode 100644 index e60c646a..00000000 --- a/modules/local/sra_to_samplesheet/tests/main.nf.test.snap +++ /dev/null @@ -1,113 +0,0 @@ -{ - "Should run without failures": { - "content": [ - { - "0": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", - "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" - ] - ], - "1": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", - "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" - ] - ], - "mappings": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", - "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.mappings.csv:md5,d09ddb4f0709675e5dfe1eadf12c608f" - ] - ], - "samplesheet": [ - [ - { - "id": "ERX1188904_ERR1109373", - "run_accession": "ERR1109373", - "experiment_accession": "ERX1188904", - "sample_accession": "SAMEA3643867", - "experiment_alias": "ena-EXPERIMENT-CAM-03-11-2015-17:01:52:847-7", - "run_alias": "ena-RUN-CAM-03-11-2015-17:01:52:847-7", - "sample_alias": "sample_56", - "study_alias": "ena-STUDY-CAM-02-11-2015-17:42:24:189-13", - "library_layout": "PAIRED", - "experiment_title": "Illumina HiSeq 2500 paired end sequencing", - "sample_title": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "sample_description": "RNA-Seq reads mapped onto L. Boulardi Toti-like virus genome", - "fastq_md5": "8d7d7b854d0207d1226477a30103fade;9fd57225d6c07a31843276d6df9b15c0;5a62e8f785687dce890cfb4fe3e607f9", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/003/ERR1109373/ERR1109373_2.fastq.gz", - "fastq_1": "./results/fastq/ERX1188904_ERR1109373_1.fastq.gz", - "fastq_2": "./results/fastq/ERX1188904_ERR1109373_2.fastq.gz", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" - ] - ] - } - ], - "timestamp": "2023-08-23T09:38:15+0000" - } -} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 4fad92ca..1e8bea6e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,27 +22,23 @@ params { dbgap_key = null // Boilerplate options - outdir = null - tracedir = "${params.outdir}/pipeline_info" - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes,igenomes_base' + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + version = false // Config options - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null - config_profile_contact = null - config_profile_url = null - config_profile_name = null + config_profile_name = null + config_profile_description = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_contact = null + config_profile_url = null // Max resource options // Defaults only, expecting to be overwritten @@ -50,6 +46,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -159,14 +162,24 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - test { - includeConfig 'conf/test.config' - includeConfig 'conf/test_data.config' - } + test { includeConfig 'conf/test.config' } test_synapse { includeConfig 'conf/test_synapse.config' } test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -181,28 +194,22 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -// Set default registry for Docker and Podman independent of -profile -// Will not be used unless Docker / Podman are enabled -// Set to your registry if you have a mirror of containers -docker.registry = 'quay.io' -podman.registry = 'quay.io' - def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -211,8 +218,8 @@ manifest { homePage = 'https://github.com/nf-core/fetchngs' description = """Pipeline to fetch metadata and raw FastQ files from public databases""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '1.10.1' + nextflowVersion = '!>=23.04.0' + version = '1.10.1dev' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/nextflow_schema.json b/nextflow_schema.json index ce2c13cc..cda974a5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,6 +15,7 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.(csv|tsv|txt)$", "schema": "assets/schema_input.json", @@ -68,7 +69,8 @@ "type": "string", "fa_icon": "fas fa-address-card", "help_text": "Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit. Users with granted access to controlled data can download the JWT cart file for the study from the SRA Run Selector upon logging in. The JWT file can only be used on cloud platforms and is valid for 1 hour upon creation.", - "format": "file-path" + "format": "file-path", + "description": "dbGaP repository key." }, "outdir": { "type": "string", @@ -168,7 +170,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -185,12 +187,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -214,12 +218,14 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "monochrome_logs": { "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -229,13 +235,6 @@ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -243,12 +242,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/nf-test.config b/nf-test.config deleted file mode 100644 index 0799cb40..00000000 --- a/nf-test.config +++ /dev/null @@ -1,16 +0,0 @@ -config { - // location for all nf-tests - testsDir "." - - // nf-test directory including temporary files for each test - workDir ".nf-test" - - // location of library folder that is added automatically to the classpath - libDir "lib/" - - // location of an optional nextflow.config file specific for executing tests - configFile "nextflow.config" - - // run all test with the defined docker profile from the main nextflow.config - profile "" -} diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test deleted file mode 100644 index 45280ab0..00000000 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ /dev/null @@ -1,33 +0,0 @@ -nextflow_workflow { - - name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_custom_ena_metadata_fields" - - test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - nf_core_pipeline = "rnaseq" - ena_metadata_fields = "run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5" - sample_mapping_fields = "run_accession,library_layout" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap deleted file mode 100644 index a2537a95..00000000 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ /dev/null @@ -1,573 +0,0 @@ -{ - 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- name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_default_parameters" - - test("Parameters: default") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_default_parameters.nf.test.snap b/workflows/sra/tests/sra_default_parameters.nf.test.snap deleted file mode 100644 index b8dc88ca..00000000 --- a/workflows/sra/tests/sra_default_parameters.nf.test.snap +++ /dev/null @@ -1,1353 +0,0 @@ -{ - "Parameters: default": { - "content": [ - { - "0": [ - [ - { - "id": "DRX024467_DRR026872", - "run_accession": "DRR026872", - "experiment_accession": "DRX024467", - "sample_accession": "SAMD00023098", - 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- name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_force_sratools_download" - - test("Parameters: --force_sratools_download") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - force_sratools_download = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap b/workflows/sra/tests/sra_force_sratools_download.nf.test.snap deleted file mode 100644 index 4e1b8aaf..00000000 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ /dev/null @@ -1,1351 +0,0 @@ -{ - "Parameters: --force_sratools_download": { - "content": [ - { - "0": [ - [ - { - "id": "DRX024467_DRR026872", - 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- name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_atacseq" - - test("Parameters: --nf_core_pipeline atacseq") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - nf_core_pipeline = "atacseq" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap deleted file mode 100644 index f6528e52..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ /dev/null @@ -1,1353 +0,0 @@ -{ - "Parameters: --nf_core_pipeline atacseq": { - "content": [ - { - "0": [ - [ - { - "id": "DRX024467_DRR026872", - 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- name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_rnaseq" - - test("Parameters: --nf_core_pipeline rnaseq") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - nf_core_pipeline = "rnaseq" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap deleted file mode 100644 index 124877ae..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ /dev/null @@ -1,1353 +0,0 @@ -{ - "Parameters: --nf_core_pipeline rnaseq": { - "content": [ - { - "0": [ - [ - { - "id": "DRX024467_DRR026872", - 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- name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_taxprofiler" - - test("Parameters: --nf_core_pipeline taxprofiler") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - nf_core_pipeline = "taxprofiler" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap deleted file mode 100644 index b63ad4b7..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ /dev/null @@ -1,1353 +0,0 @@ -{ - "Parameters: --nf_core_pipeline taxprofiler": { - "content": [ - { - 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- name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_viralrecon" - - test("Parameters: --nf_core_pipeline viralrecon") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - nf_core_pipeline = "viralrecon" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap deleted file mode 100644 index 1387f422..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ /dev/null @@ -1,1353 +0,0 @@ -{ - "Parameters: --nf_core_pipeline viralrecon": { - "content": [ - { - "0": [ - 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"SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04" - ] - ], - [ - { - "id": "SRX9626017_SRR13191702", - "run_accession": "SRR13191702", - "experiment_accession": "SRX9626017", - "sample_accession": "SAMN16980141", - "secondary_sample_accession": "SRS7827211", - "study_accession": "PRJNA682076", - "secondary_study_accession": "SRP295653", - "submission_accession": "SRA1166126", - "run_alias": "S.170804.00784_662_L001_R1_001.fastq.gz", - "experiment_alias": "S.170804.00784", - "sample_alias": "S.170804.00784_662", - "study_alias": "PRJNA682076", - "library_layout": "PAIRED", - "library_selection": "PCR", - "library_source": "METAGENOMIC", - "library_strategy": "AMPLICON", - "library_name": "S.170804.00784", - "instrument_model": "Illumina HiSeq 2500", - "instrument_platform": "ILLUMINA", - "base_count": "45682", - "read_count": "91", - "tax_id": "408170", - "scientific_name": "human gut metagenome", - "sample_title": "Metagenome or environmental sample from human gut metagenome", - "experiment_title": "Illumina HiSeq 2500 sequencing: Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", - "study_title": "Stool Microbiome Features to Discriminate Clostridium Difficile Colonization and Infection", - "sample_description": "Metagenome or environmental sample from human gut metagenome", - "fastq_md5": "89c5be920021a035084d8aeb74f32df7;56271be38a80db78ef3bdfc5d9909b98", - "fastq_bytes": "15420;16324", - "fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_galaxy": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_aspera": "fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "fastq_1": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz", - "fastq_2": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz", - "md5_1": "89c5be920021a035084d8aeb74f32df7", - "md5_2": "56271be38a80db78ef3bdfc5d9909b98", - "single_end": false - }, - [ - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98" - ] - ] - ], - "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" - ], - "samplesheet": [ - "samplesheet.csv:md5,4aec9029e063bae998b3fa3dc3481556" - ], - "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,45e4a369df2d3af023b8622aa3f6d5a8", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,e977678bd13a54fc9c31addf135be15e", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" - ] - } - ], - "timestamp": "2023-09-11T18:34:25.049818" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test b/workflows/sra/tests/sra_skip_fastq_download.nf.test deleted file mode 100644 index 67abee3b..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ /dev/null @@ -1,31 +0,0 @@ -nextflow_workflow { - - name "Test workflow: sra/main.nf" - script "workflows/sra/main.nf" - workflow "SRA" - tag "workflows" - tag "workflows_sra" - tag "sra_skip_fastq_download" - - test("Parameters: --skip_fastq_download") { - - when { - workflow { - """ - input[0] = Channel.from('DRR026872','DRR028935','ERR1109373','ERR1160846','GSE214215','GSM4907283','SRR12848126','SRR13191702','SRR14593545','SRR14709033','SRR9984183') - """ - } - params { - outdir = "results" - skip_fastq_download = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(workflow.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap b/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap deleted file mode 100644 index 3b04b917..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ /dev/null @@ -1,37 +0,0 @@ -{ - "Parameters: --skip_fastq_download": { - "content": [ - { - "0": [ - - ], - "1": [ - "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" - ], - "2": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" - ], - "3": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" - ], - "fastq": [ - - ], - "mappings": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565" - ], - "samplesheet": [ - "samplesheet.csv:md5,7cf3503b651fe016bc1e5fb3c2e996d5" - ], - "versions": [ - "versions.yml:md5,b52279f7d6b891a6523d9321f3f85b47", - "versions.yml:md5,9b17045ca8bdc272cb3f9d349a81d206", - "versions.yml:md5,b21338b74b9a8fe0c7a114f7686c07cd" - ] - } - ], - "timestamp": "2023-09-11T18:56:34.175665" - } -} \ No newline at end of file diff --git a/workflows/synapse/tests/main.nf.test b/workflows/synapse/tests/main.nf.test deleted file mode 100644 index 7cbfed11..00000000 --- a/workflows/synapse/tests/main.nf.test +++ /dev/null @@ -1,28 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: synapse.nf" - script "main.nf" - tag "workflows" - tag "synapse" - tag "synapse_default" - profile "test_synapse" - - test("Synapse Input Type") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(path("$outputDir/pipeline_info/software_versions.yml")).match("software_versions") }, - { assert snapshot(path("$outputDir/samplesheet/").list()).match("samplesheet") } - ) - } - - } - -} diff --git a/workflows/synapse/tests/main.nf.test.snap b/workflows/synapse/tests/main.nf.test.snap deleted file mode 100644 index 9b25ee0c..00000000 --- a/workflows/synapse/tests/main.nf.test.snap +++ /dev/null @@ -1,16 +0,0 @@ -{ - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548", - "samplesheet.csv:md5,296e139d533c7a67567dd073ec0f945a" - ], - "timestamp": "2023-09-11T17:08:51.001588" - }, - "software_versions": { - "content": [ - "software_versions.yml:md5,966251d4b7717464ccea77d6e8841e58" - ], - "timestamp": "2023-09-11T17:08:50.994607" - } -} \ No newline at end of file