From e6afbffd26b109d648446667c6275000bf3dc2c9 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:12:44 +0000 Subject: [PATCH 1/8] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CHANGELOG.md | 2 +- CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-fetchngs_logo_light.png | Bin 11380 -> 75527 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowFetchngs.groovy | 45 +- lib/WorkflowMain.groovy | 37 -- main.nf | 16 + nextflow.config | 54 ++- nextflow_schema.json | 36 +- workflows/fetchngs.nf | 25 +- 23 files changed, 177 insertions(+), 639 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy 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/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 523b1033..f21cdd8a 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/fetchngs/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index cdfba2f0..3b549466 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/fetchngs/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/fetchngs/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f0e03c7b..857350a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code 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/CHANGELOG.md b/CHANGELOG.md index 2792d527..40fa6636 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.10dev - [date] +## v1.10.1 - [date] Initial release of nf-core/fetchngs, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 1854d6e6..92d2ad5a 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [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. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [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 c229c26c..22d5f2ee 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.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![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/) @@ -66,11 +66,11 @@ 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). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/fetchngs/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/fetchngs/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/fetchngs/output). 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..70cc1fc7 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. 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z2?tWK@X0WhGf98kBaVM2SuRjIWkvY9&sD(zT+?JjSCqm0L670@R*TGau%=30nZSP= zcaJV7ERx@!L{q4>6A6J%)Sn5w3`BAo?tYmv4ft>O-_1iwe#8-a7c7VD8gS32v4#+q zZ(jFQKtZS&7>Ty6={o-9ryLKFlD$=|dG77f-VU|8bT2}1vmSdFk3w1QF)ZF9K zd#iCB=;ek3good<% } else { %>danger<%} %>", - "author_name": "sanger-tol/readmapping v${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/conf/test_full.config b/conf/test_full.config index 4c032754..460f61d4 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 efd5e798..2772f340 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/fetchngs --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/fetchngs --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/fetchngs -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` 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."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowFetchngs.groovy b/lib/WorkflowFetchngs.groovy index 748aaa28..90656882 100755 --- a/lib/WorkflowFetchngs.groovy +++ b/lib/WorkflowFetchngs.groovy @@ -11,6 +11,7 @@ class WorkflowFetchngs { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowFetchngs { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index f1dcf537..a404118e 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -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) { @@ -62,14 +33,6 @@ 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 4da08510..5a857bde 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index a7d70e06..f37501fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + 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_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ 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 @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/fetchngs profiles: ${params.custom_config_base}/pipeline/fetchngs.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${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_${trace_timestamp}.html" } manifest { @@ -219,8 +227,8 @@ manifest { homePage = 'https://github.com/nf-core/fetchngs' description = """Pipeline to fetch metadata and raw FastQ files from public databases""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '1.10dev' + nextflowVersion = '!>=23.04.0' + version = '1.10.1' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index b0720ed5..fec3af4a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/fetchngs/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${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", @@ -257,12 +256,29 @@ "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/workflows/fetchngs.nf b/workflows/fetchngs.nf index 4cb46a27..683f2748 100644 --- a/workflows/fetchngs.nf +++ b/workflows/fetchngs.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowFetchngs.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowFetchngs.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow FETCHNGS { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow FETCHNGS { workflow_summary = WorkflowFetchngs.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowFetchngs.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowFetchngs.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 4bec2990de02ed84c3df5d37acea8a70e46a3934 Mon Sep 17 00:00:00 2001 From: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Date: Thu, 21 Sep 2023 10:29:23 +0100 Subject: [PATCH 2/8] Revert dev to release 1.10 This reverts commit 624d420ecbb1f039695132fa02db78fcd65002f6, reversing changes made to 1b9d1876b3973e436618652ffa485395f8f57213. --- .gitattributes | 1 - .github/workflows/ci.yml | 82 ++++------ .gitignore | 2 - .nf-core.yml | 10 -- CHANGELOG.md | 16 -- bin/sra_runinfo_to_ftp.py | 3 +- conf/test.config | 3 - conf/test_data.config | 36 ----- docs/usage.md | 6 - lib/NftestUtils.groovy | 38 ----- modules.json | 3 +- .../main.nf => multiqc_mappings_config.nf} | 0 .../tests/main.nf.test | 31 ---- .../tests/main.nf.test.snap | 52 ------- .../main.nf => sra_fastq_ftp.nf} | 0 .../local/sra_fastq_ftp/tests/main.nf.test | 34 ----- .../sra_fastq_ftp/tests/main.nf.test.snap | 140 ------------------ .../main.nf => sra_ids_to_runinfo.nf} | 0 .../sra_ids_to_runinfo/tests/main.nf.test | 32 ---- .../tests/main.nf.test.snap | 21 --- .../main.nf => sra_merge_samplesheet.nf} | 0 .../sra_merge_samplesheet/tests/main.nf.test | 32 ---- .../tests/main.nf.test.snap | 27 ---- .../main.nf => sra_runinfo_to_ftp.nf} | 0 .../sra_runinfo_to_ftp/tests/main.nf.test | 31 ---- .../tests/main.nf.test.snap | 21 --- .../main.nf => sra_to_samplesheet.nf} | 0 .../sra_to_samplesheet/tests/main.nf.test | 34 ----- .../tests/main.nf.test.snap | 113 -------------- .../{synapse_get/main.nf => synapse_get.nf} | 0 .../{synapse_list/main.nf => synapse_list.nf} | 0 .../main.nf => synapse_merge_samplesheet.nf} | 0 .../{synapse_show/main.nf => synapse_show.nf} | 0 .../main.nf => synapse_to_samplesheet.nf} | 0 .../custom-dumpsoftwareversions.diff | 13 -- .../templates/dumpsoftwareversions.py | 1 + nextflow.config | 2 +- nf-test.config | 16 -- workflows/{sra/main.nf => sra.nf} | 16 +- workflows/sra/tests/main.nf.test | 24 --- workflows/sra/tests/main.nf.test.snap | 88 ----------- .../sra_custom_ena_metadata_fields.nf.test | 27 ---- ...ra_custom_ena_metadata_fields.nf.test.snap | 88 ----------- .../tests/sra_force_sratools_download.nf.test | 25 ---- .../sra_force_sratools_download.nf.test.snap | 67 --------- .../sra_nf_core_pipeline_atacseq.nf.test | 25 ---- .../sra_nf_core_pipeline_atacseq.nf.test.snap | 88 ----------- .../tests/sra_nf_core_pipeline_rnaseq.nf.test | 25 ---- .../sra_nf_core_pipeline_rnaseq.nf.test.snap | 88 ----------- .../sra_nf_core_pipeline_taxprofiler.nf.test | 25 ---- ..._nf_core_pipeline_taxprofiler.nf.test.snap | 88 ----------- .../sra_nf_core_pipeline_viralrecon.nf.test | 25 ---- ...a_nf_core_pipeline_viralrecon.nf.test.snap | 88 ----------- .../sra/tests/sra_skip_fastq_download.nf.test | 25 ---- .../sra_skip_fastq_download.nf.test.snap | 46 ------ workflows/{synapse/main.nf => synapse.nf} | 12 +- workflows/synapse/tests/main.nf.test | 28 ---- 57 files changed, 47 insertions(+), 1651 deletions(-) delete mode 100644 conf/test_data.config delete mode 100644 lib/NftestUtils.groovy rename modules/local/{multiqc_mappings_config/main.nf => multiqc_mappings_config.nf} (100%) delete mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test delete mode 100644 modules/local/multiqc_mappings_config/tests/main.nf.test.snap rename modules/local/{sra_fastq_ftp/main.nf => sra_fastq_ftp.nf} (100%) delete mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test delete mode 100644 modules/local/sra_fastq_ftp/tests/main.nf.test.snap rename modules/local/{sra_ids_to_runinfo/main.nf => sra_ids_to_runinfo.nf} (100%) delete mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test delete mode 100644 modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap rename modules/local/{sra_merge_samplesheet/main.nf => sra_merge_samplesheet.nf} (100%) delete mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test delete mode 100644 modules/local/sra_merge_samplesheet/tests/main.nf.test.snap rename modules/local/{sra_runinfo_to_ftp/main.nf => sra_runinfo_to_ftp.nf} (100%) delete mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test delete mode 100644 modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap rename modules/local/{sra_to_samplesheet/main.nf => sra_to_samplesheet.nf} (100%) delete mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test delete mode 100644 modules/local/sra_to_samplesheet/tests/main.nf.test.snap rename modules/local/{synapse_get/main.nf => synapse_get.nf} (100%) rename modules/local/{synapse_list/main.nf => synapse_list.nf} (100%) rename modules/local/{synapse_merge_samplesheet/main.nf => synapse_merge_samplesheet.nf} (100%) rename modules/local/{synapse_show/main.nf => synapse_show.nf} (100%) rename modules/local/{synapse_to_samplesheet/main.nf => synapse_to_samplesheet.nf} (100%) delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff delete mode 100644 nf-test.config rename workflows/{sra/main.nf => sra.nf} (89%) delete mode 100644 workflows/sra/tests/main.nf.test delete mode 100644 workflows/sra/tests/main.nf.test.snap delete mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test delete mode 100644 workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap delete mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test delete mode 100644 workflows/sra/tests/sra_force_sratools_download.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test delete mode 100644 workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test delete mode 100644 workflows/sra/tests/sra_skip_fastq_download.nf.test.snap rename workflows/{synapse/main.nf => synapse.nf} (89%) delete mode 100644 workflows/synapse/tests/main.nf.test 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/workflows/ci.yml b/.github/workflows/ci.yml index 451613fb..5bef3edd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,61 +1,31 @@ -# 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: push: branches: - dev pull_request: - branches: - - dev - - master release: - types: - - "published" + types: [published] env: NXF_ANSI_LOG: false - NFTEST_VER: "0.7.3" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true jobs: - 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 $GITHUB_OUTPUT - fi - test: name: Run pipeline with test data - needs: define_nxf_versions + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}" runs-on: ubuntu-latest strategy: - fail-fast: false matrix: - NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} - test_tags: - - "modules_local" - - "sra_default_parameters" - - "sra_custom_ena_metadata_fields" - - "sra_force_sratools_download" - - "sra_nf_core_pipeline_atacseq" - - "sra_nf_core_pipeline_rnaseq" - - "sra_nf_core_pipeline_taxprofiler" - - "sra_nf_core_pipeline_viralrecon" - - "sra_skip_fastq_download" - profile: - - "docker" - + NXF_VER: + - "22.10.1" + - "latest-everything" steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -65,23 +35,29 @@ jobs: with: version: "${{ 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 ${{ matrix.test_tags }} --profile "test,${{ 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/*/output/pipeline_info/software_versions.yml - - - 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 935326a7..5124c9ac 100644 --- a/.gitignore +++ b/.gitignore @@ -6,5 +6,3 @@ results/ testing/ testing* *.pyc -.nf-test/ -nf-test diff --git a/.nf-core.yml b/.nf-core.yml index 253f86e2..cafd671c 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,15 +1,5 @@ repository_type: pipeline lint: 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 - actions_ci: false - multiqc_config: false - nextflow_config: - - "params.validationShowHiddenParams" - - "params.validationSchemaIgnoreParams" - schema_params: false diff --git a/CHANGELOG.md b/CHANGELOG.md index 146b93b6..12ef2d50 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,22 +3,6 @@ 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 - ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 ### Credits 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 0bc98595..3c58e9cf 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,6 +22,3 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv' } - -// Load test_data.config for nf-tests -includeConfig 'test_data.config' 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/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/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/modules.json b/modules.json index 2244addd..3137b88b 100644 --- a/modules.json +++ b/modules.json @@ -8,8 +8,7 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"], - "patch": "modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff" + "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", diff --git a/modules/local/multiqc_mappings_config/main.nf b/modules/local/multiqc_mappings_config.nf similarity index 100% rename from modules/local/multiqc_mappings_config/main.nf rename to modules/local/multiqc_mappings_config.nf 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/main.nf b/modules/local/sra_fastq_ftp.nf similarity index 100% rename from modules/local/sra_fastq_ftp/main.nf rename to modules/local/sra_fastq_ftp.nf 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/main.nf b/modules/local/sra_ids_to_runinfo.nf similarity index 100% rename from modules/local/sra_ids_to_runinfo/main.nf rename to modules/local/sra_ids_to_runinfo.nf 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/main.nf b/modules/local/sra_merge_samplesheet.nf similarity index 100% rename from modules/local/sra_merge_samplesheet/main.nf rename to modules/local/sra_merge_samplesheet.nf 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/main.nf b/modules/local/sra_runinfo_to_ftp.nf similarity index 100% rename from modules/local/sra_runinfo_to_ftp/main.nf rename to modules/local/sra_runinfo_to_ftp.nf 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/main.nf b/modules/local/sra_to_samplesheet.nf similarity index 100% rename from modules/local/sra_to_samplesheet/main.nf rename to modules/local/sra_to_samplesheet.nf 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 8b5f4947..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": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "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": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "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": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "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": "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "fastq_2": "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "md5_1": "9fd57225d6c07a31843276d6df9b15c0", - "md5_2": "5a62e8f785687dce890cfb4fe3e607f9", - "single_end": false - }, - "ERX1188904_ERR1109373.samplesheet.csv:md5,e7898191d57258e049ee7129d36f5c08" - ] - ] - } - ], - "timestamp": "2023-08-17T10:55:52+0000" - } -} \ No newline at end of file diff --git a/modules/local/synapse_get/main.nf b/modules/local/synapse_get.nf similarity index 100% rename from modules/local/synapse_get/main.nf rename to modules/local/synapse_get.nf diff --git a/modules/local/synapse_list/main.nf b/modules/local/synapse_list.nf similarity index 100% rename from modules/local/synapse_list/main.nf rename to modules/local/synapse_list.nf diff --git a/modules/local/synapse_merge_samplesheet/main.nf b/modules/local/synapse_merge_samplesheet.nf similarity index 100% rename from modules/local/synapse_merge_samplesheet/main.nf rename to modules/local/synapse_merge_samplesheet.nf diff --git a/modules/local/synapse_show/main.nf b/modules/local/synapse_show.nf similarity index 100% rename from modules/local/synapse_show/main.nf rename to modules/local/synapse_show.nf diff --git a/modules/local/synapse_to_samplesheet/main.nf b/modules/local/synapse_to_samplesheet.nf similarity index 100% rename from modules/local/synapse_to_samplesheet/main.nf rename to modules/local/synapse_to_samplesheet.nf diff --git a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff b/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff deleted file mode 100644 index a7893b24..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/custom-dumpsoftwareversions.diff +++ /dev/null @@ -1,13 +0,0 @@ -Changes in module 'nf-core/custom/dumpsoftwareversions' ---- modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -+++ modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py -@@ -75,7 +75,6 @@ - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { -- "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - -************************************************************ diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index 33d127f8..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -75,6 +75,7 @@ def main(): versions_by_module[module] = process_versions versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", "$workflow.manifest.name": "$workflow.manifest.version", } diff --git a/nextflow.config b/nextflow.config index 6eb5c18d..1e9aaed0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -212,7 +212,7 @@ manifest { description = """Pipeline to fetch metadata and raw FastQ files from public databases""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.10.1' + version = '1.10.0' doi = 'https://doi.org/10.5281/zenodo.5070524' } 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/main.nf b/workflows/sra.nf similarity index 89% rename from workflows/sra/main.nf rename to workflows/sra.nf index 512a73d4..44ff8346 100644 --- a/workflows/sra/main.nf +++ b/workflows/sra.nf @@ -19,12 +19,12 @@ WorkflowSra.initialise(params, valid_params) ======================================================================================== */ -include { SRA_IDS_TO_RUNINFO } from '../../modules/local/sra_ids_to_runinfo' -include { SRA_RUNINFO_TO_FTP } from '../../modules/local/sra_runinfo_to_ftp' -include { SRA_FASTQ_FTP } from '../../modules/local/sra_fastq_ftp' -include { SRA_TO_SAMPLESHEET } from '../../modules/local/sra_to_samplesheet' -include { SRA_MERGE_SAMPLESHEET } from '../../modules/local/sra_merge_samplesheet' -include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config' +include { SRA_IDS_TO_RUNINFO } from '../modules/local/sra_ids_to_runinfo' +include { SRA_RUNINFO_TO_FTP } from '../modules/local/sra_runinfo_to_ftp' +include { SRA_FASTQ_FTP } from '../modules/local/sra_fastq_ftp' +include { SRA_TO_SAMPLESHEET } from '../modules/local/sra_to_samplesheet' +include { SRA_MERGE_SAMPLESHEET } from '../modules/local/sra_merge_samplesheet' +include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config' /* ======================================================================================== @@ -32,9 +32,9 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' -include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools' +include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main' /* ======================================================================================== diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test deleted file mode 100644 index 39a5cc3f..00000000 --- a/workflows/sra/tests/main.nf.test +++ /dev/null @@ -1,24 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_default_parameters" - - test("Parameters: default") { - - when { - params { - outdir = "$outputDir" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.out).match() } - ) - } - } -} diff --git a/workflows/sra/tests/main.nf.test.snap b/workflows/sra/tests/main.nf.test.snap deleted file mode 100644 index 88ea9654..00000000 --- a/workflows/sra/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "Parameters: default": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:09:45+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:09:45+0000" - } -} \ No newline at end of file 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 6e27c4a9..00000000 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test +++ /dev/null @@ -1,27 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_custom_ena_metadata_fields" - - test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") { - - when { - params { - outdir = "$outputDir" - 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(process.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 55c39d4f..00000000 --- a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,74a5f7058f27a565ce59db481355ca54", - "DRR028935.runinfo_ftp.tsv:md5,07a98fdcec207686a4ea2c9a3997edf3", - "ERR1109373.runinfo_ftp.tsv:md5,868897310855c50b1d5fc77d1195a1f9", - "ERR1160846.runinfo_ftp.tsv:md5,146d7f2ec778b32b7da7ad040e554114", - "GSE214215.runinfo_ftp.tsv:md5,adf62affe371dc9bad8e271450bdc2fe", - "SRR12848126.runinfo_ftp.tsv:md5,cf8827612a76645824e83418d7d76cbf", - "SRR13191702.runinfo_ftp.tsv:md5,2031ca9b7ab736dbde37d05b10cdb0ad", - "SRR14593545.runinfo_ftp.tsv:md5,3a1ac14d71744224a61ab542f869e180", - "SRR14709033.runinfo_ftp.tsv:md5,2385a9cc5e320e78b02743c45d1338f1", - "SRR9984183.runinfo_ftp.tsv:md5,f1ed9fc572d2e0d145be7f547f6d1236" - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,8473773df806859c6af7acafcfe5aa6f", - "multiqc_config.yml:md5,6f6189ee58855de81eaf82ad86e21040" - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "Parameters: '--nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:11:42+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:11:42+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test deleted file mode 100644 index 1b501975..00000000 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_force_sratools_download" - - test("Parameters: --force_sratools_download") { - - when { - params { - outdir = "$outputDir" - force_sratools_download = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.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 d5d694da..00000000 --- a/workflows/sra/tests/sra_force_sratools_download.nf.test.snap +++ /dev/null @@ -1,67 +0,0 @@ -{ - "Parameters: '--force_sratools_download'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:15:55+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,bd3f113c3b06cf4499fa0e00c634ec85", - "DRX026011_DRR028935_1.fastq.gz:md5,0f96fb60e903c8cbd55a6977e66f7c93", - "DRX026011_DRR028935_2.fastq.gz:md5,b97b1e0e806bcae10a7443e2f22d6ca2", - "ERX1188904_ERR1109373_1.fastq.gz:md5,e7edae2715dfaf4c318d37959fd9ae22", - "ERX1188904_ERR1109373_2.fastq.gz:md5,34ab048c92201a5ec4ab36d8dc1c5732", - "ERX1234253_ERR1160846.fastq.gz:md5,22683b24b2467494e430643423f1e275", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,eae43f1368d4568f415581394dc9726e", - "SRX17709228_SRR21711855.fastq.gz:md5,5194f8009b74552595c4ec5b7605d231", - "SRX6725035_SRR9984183.fastq.gz:md5,7a70e678c400366869601c8be41fe74b", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,b6d912a73466c8f27b1d8021f80ec2bb", - "SRX9504942_SRR13055517_2.fastq.gz:md5,7c6e220694fa5d6d9124c739aa70ea92", - "SRX9504942_SRR13055518_1.fastq.gz:md5,ed29278c21a1bb2d8907a74be0dd4bc4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,83785b728312deb81483fc1fd5b14264", - "SRX9504942_SRR13055519_1.fastq.gz:md5,28babc59a625b5161d97392efd4d0018", - "SRX9504942_SRR13055519_2.fastq.gz:md5,cf1eb4c61ab3522f4d473c86b2f696e1", - "SRX9504942_SRR13055520_1.fastq.gz:md5,cc75af896ec8a7cececb37851b0c6fcd", - "SRX9504942_SRR13055520_2.fastq.gz:md5,fe3e2bf9f738e4959243fad59e879eae", - "SRX9626017_SRR13191702_1.fastq.gz:md5,627a90afcd9f3cfc7f5f91074f9a2df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,3d9b2c68a8ad1547105b17de81b2d9af" - ], - "timestamp": "2023-08-17T12:15:55+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test deleted file mode 100644 index bda1d724..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_atacseq" - - test("Parameters: --nf_core_pipeline atacseq") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "atacseq" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.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 c99f258e..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "Parameters: '--nf_core_pipeline atacseq'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:21:36+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:21:36+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test deleted file mode 100644 index 438b7f55..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_rnaseq" - - test("Parameters: --nf_core_pipeline rnaseq") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "rnaseq" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.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 1da0381a..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "Parameters: '--nf_core_pipeline rnaseq'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:19:51+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:19:51+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test deleted file mode 100644 index 301938c4..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_taxprofiler" - - test("Parameters: --nf_core_pipeline taxprofiler") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "taxprofiler" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.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 85f3957b..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "Parameters: --nf_core_pipeline taxprofiler": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:24:34+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - 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"SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - 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] - ], - "timestamp": "2023-08-17T12:24:34+0000" - } -} \ No newline at end of file diff --git a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test b/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test deleted file mode 100644 index 892a7c3a..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_nf_core_pipeline_viralrecon" - - test("Parameters: --nf_core_pipeline viralrecon") { - - when { - params { - outdir = "$outputDir" - nf_core_pipeline = "viralrecon" - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.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 13c59b5d..00000000 --- a/workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "Parameters: --nf_core_pipeline viralrecon": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_SRATOOLSNCBISETTINGS={sratools=2.11.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_FASTQ_FTP={curl=7.81.0}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:26:57+0000" - }, - "fastq": { - "content": [ - "DRX024467_DRR026872.fastq.gz:md5,515e5448c55e054113c4a22df5f62791", - "DRX026011_DRR028935_1.fastq.gz:md5,cc01df82a9354bb6b3be93483b20c35a", - "DRX026011_DRR028935_2.fastq.gz:md5,941c9998d746416dad53c94c480ddf30", - "ERX1188904_ERR1109373_1.fastq.gz:md5,9fd57225d6c07a31843276d6df9b15c0", - "ERX1188904_ERR1109373_2.fastq.gz:md5,5a62e8f785687dce890cfb4fe3e607f9", - "ERX1234253_ERR1160846.fastq.gz:md5,5924f20ef547ebdfed7cad795bbab6e6", - "SRX10940790_SRR14593545_1.fastq.gz:md5,6a4762cf0f1f9f5544d3735e2e07c5d3", - "SRX10940790_SRR14593545_2.fastq.gz:md5,cbd30715fdef457d7aa24a12f19eedf2", - "SRX11047067_SRR14709033.fastq.gz:md5,79140dd1cb3fd1c5e02d88e01f7c3eda", - "SRX17709227_SRR21711856.fastq.gz:md5,7cd1402155befc87be338132d1f31f64", - "SRX17709228_SRR21711855.fastq.gz:md5,cbe4e9f967a71593f9ec3c6edaf11c83", - "SRX6725035_SRR9984183.fastq.gz:md5,0b512d2dc31685983456bd56fd836544", - "SRX9315476_SRR12848126_1.fastq.gz:md5,03f5a34586aef9cd61f54eb26831a665", - "SRX9315476_SRR12848126_2.fastq.gz:md5,97701c5d884af8d96ba95d7237f3bf79", - "SRX9504942_SRR13055517_1.fastq.gz:md5,dcf4438c0b682242ee90c5f3a803fb40", - "SRX9504942_SRR13055517_2.fastq.gz:md5,18dbe96e7f58b63406d9058938df1962", - "SRX9504942_SRR13055518_1.fastq.gz:md5,5ec894d863fcefe394470a0925aefde4", - "SRX9504942_SRR13055518_2.fastq.gz:md5,aead170df9851773d5202b5760c76d76", - "SRX9504942_SRR13055519_1.fastq.gz:md5,5ad51460c6c4a850dd37a206e2c441c1", - "SRX9504942_SRR13055519_2.fastq.gz:md5,a977367bf41dacf4c21bc0c8201b8b88", - "SRX9504942_SRR13055520_1.fastq.gz:md5,795d460abff6009c7f5ff7c14b773fbe", - "SRX9504942_SRR13055520_2.fastq.gz:md5,c3f34379356b28d6dac7212abc1a0a04", - "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7", - "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98", - [ - "DRX024467_DRR026872.fastq.gz.md5:md5,dacaeba3498fb8f405411a22cdb4b40d", - "DRX026011_DRR028935_1.fastq.gz.md5:md5,a47018c5972ba4c11539d0d6bc25eda9", - "DRX026011_DRR028935_2.fastq.gz.md5:md5,f477bbef548fbed665734ebf084eea2f", - "ERX1188904_ERR1109373_1.fastq.gz.md5:md5,50c1c3108631dc32a3151b67e0260d86", - "ERX1188904_ERR1109373_2.fastq.gz.md5:md5,1f22463d410e91a288c83d43654b2499", - "ERX1234253_ERR1160846.fastq.gz.md5:md5,513a8437ad331fc512b088b3750aa1ff", - "SRX17709227_SRR21711856.fastq.gz.md5:md5,13a38fbef27c3e15867d80887145ae75", - "SRX17709228_SRR21711855.fastq.gz.md5:md5,1e871ddd9e92e1866e0c64d36eb5ec85", - "SRX6725035_SRR9984183.fastq.gz.md5:md5,84f59dbb76c9b5eab7e14d90ced352c4", - "SRX9504942_SRR13055517_1.fastq.gz.md5:md5,a03f7f374dc401047b6f6ccaec3885cc", - "SRX9504942_SRR13055517_2.fastq.gz.md5:md5,facaf207753e977327e7b7df7bb8ace0", - "SRX9504942_SRR13055518_1.fastq.gz.md5:md5,5cf412cd62aadaa4838d9eabb5b44368", - "SRX9504942_SRR13055518_2.fastq.gz.md5:md5,93292b826afc72b23be93df26dd710c8", - "SRX9504942_SRR13055519_1.fastq.gz.md5:md5,f6ad6e2610397147a0a55c651de3992f", - "SRX9504942_SRR13055519_2.fastq.gz.md5:md5,2fe7dd4bcc1e7e61c6f54ef50cf961f3", - "SRX9504942_SRR13055520_1.fastq.gz.md5:md5,ab195b37746a3424a1099d9f8cc58de8", - "SRX9504942_SRR13055520_2.fastq.gz.md5:md5,10c448e23f1f7e7af61ec1204f8fc882", - "SRX9626017_SRR13191702_1.fastq.gz.md5:md5,055a6916ec9ee478e453d50651f87997", - "SRX9626017_SRR13191702_2.fastq.gz.md5:md5,c30ac785f8d80ec563fabf604d8bf945" - ] - ], - "timestamp": "2023-08-17T12:26:57+0000" - } -} \ 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 7d218cf7..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test +++ /dev/null @@ -1,25 +0,0 @@ -nextflow_pipeline { - - name "Test workflow: sra.nf" - script "main.nf" - tag "workflows" - tag "workflows_sra" - tag "sra_skip_fastq_download" - - test("Parameters: --skip_fastq_download") { - - when { - params { - outdir = "$outputDir" - skip_fastq_download = true - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot(process.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 d004d5d2..00000000 --- a/workflows/sra/tests/sra_skip_fastq_download.nf.test.snap +++ /dev/null @@ -1,46 +0,0 @@ -{ - "Parameters: '--skip_fastq_download'": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "metadata": { - "content": [ - "DRR026872.runinfo_ftp.tsv:md5,73606f6a05c45b077809da43ca638b5f", - "DRR028935.runinfo_ftp.tsv:md5,f79eefcea5db346f76f76f87df7f8dd2", - "ERR1109373.runinfo_ftp.tsv:md5,d1717cb1638950b7af22ec1b976616a4", - "ERR1160846.runinfo_ftp.tsv:md5,1b2dc1a64117de20b2164724836da345", - "GSE214215.runinfo_ftp.tsv:md5,23a580c89ee7bf681ca3ffa26aa1837f", - "SRR12848126.runinfo_ftp.tsv:md5,5d1e6bfd3d4077d1e66378c58e44975d", - "SRR13191702.runinfo_ftp.tsv:md5,409e262bb41bb6103315126db4d0dd1d", - "SRR14593545.runinfo_ftp.tsv:md5,62015706ac156693ba3d86ed050cab54", - "SRR14709033.runinfo_ftp.tsv:md5,975dd9b32bdbd78b5da3cd88a5f705c1", - "SRR9984183.runinfo_ftp.tsv:md5,53ab34ff3612b0e2c7d60476822787be" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "samplesheet": { - "content": [ - "id_mappings.csv:md5,3e287081f1e9349921fa8c709a874565", - "multiqc_config.yml:md5,a97047e12b0ea3f46d285629e4053548" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "software_versions": { - "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, MULTIQC_MAPPINGS_CONFIG={python=3.9.5}, SRA_IDS_TO_RUNINFO={python=3.9.5}, SRA_MERGE_SAMPLESHEET={sed=4.7}, SRA_RUNINFO_TO_FTP={python=3.9.5}, Workflow={nf-core/fetchngs=1.10.1}}" - ], - "timestamp": "2023-08-17T12:25:19+0000" - }, - "Parameters: --skip_fastq_download": { - "content": [ - { - - } - ], - "timestamp": "2023-08-17T12:25:19+0000" - } -} \ No newline at end of file diff --git a/workflows/synapse/main.nf b/workflows/synapse.nf similarity index 89% rename from workflows/synapse/main.nf rename to workflows/synapse.nf index f8cbeba1..f2138a60 100644 --- a/workflows/synapse/main.nf +++ b/workflows/synapse.nf @@ -19,11 +19,11 @@ if (params.synapse_config) { ======================================================================================== */ -include { SYNAPSE_LIST } from '../../modules/local/synapse_list' -include { SYNAPSE_SHOW } from '../../modules/local/synapse_show' -include { SYNAPSE_GET } from '../../modules/local/synapse_get' -include { SYNAPSE_TO_SAMPLESHEET } from '../../modules/local/synapse_to_samplesheet' -include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_samplesheet' +include { SYNAPSE_LIST } from '../modules/local/synapse_list' +include { SYNAPSE_SHOW } from '../modules/local/synapse_show' +include { SYNAPSE_GET } from '../modules/local/synapse_get' +include { SYNAPSE_TO_SAMPLESHEET } from '../modules/local/synapse_to_samplesheet' +include { SYNAPSE_MERGE_SAMPLESHEET } from '../modules/local/synapse_merge_samplesheet' /* ======================================================================================== @@ -31,7 +31,7 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa ======================================================================================== */ -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ======================================================================================== 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") } - ) - } - - } - -} From e93c45a9f5fa1c16183e924e99ba4e41539bc328 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 12:31:25 +0200 Subject: [PATCH 3/8] fix nf-core linting --- assets/multiqc_config.yml | 4 ++-- modules.json | 22 ++++++++++++++++------ nextflow.config | 7 ------- nextflow_schema.json | 18 ------------------ 4 files changed, 18 insertions(+), 33 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 70cc1fc7..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/modules.json b/modules.json index 3137b88b..2daacf3a 100644 --- a/modules.json +++ b/modules.json @@ -8,22 +8,30 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/sratoolsncbisettings": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": [ + "fastq_download_prefetch_fasterqdump_sratools" + ] }, "sratools/fasterqdump": { "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": [ + "fastq_download_prefetch_fasterqdump_sratools" + ] }, "sratools/prefetch": { "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", - "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] + "installed_by": [ + "fastq_download_prefetch_fasterqdump_sratools" + ] } } }, @@ -32,10 +40,12 @@ "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 9caf9ff2..2a8e9bcc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -21,13 +21,6 @@ params { skip_fastq_download = false dbgap_key = null - // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null - // Boilerplate options outdir = null publish_dir_mode = 'copy' diff --git a/nextflow_schema.json b/nextflow_schema.json index 3816846f..def56011 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -234,24 +234,6 @@ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, - "multiqc_config": { - "type": "string", - "format": "file-path", - "description": "Custom config file to supply to MultiQC.", - "fa_icon": "fas fa-cog", - "hidden": true - }, - "multiqc_logo": { - "type": "string", - "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", - "fa_icon": "fas fa-image", - "hidden": true - }, - "multiqc_methods_description": { - "type": "string", - "description": "Custom MultiQC yaml file containing HTML including a methods description.", - "fa_icon": "fas fa-cog" - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", From 797a15bfc0afad3eb0a9a628b5fb8d588baa6873 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 14:14:42 +0200 Subject: [PATCH 4/8] syntax fix --- lib/NfcoreTemplate.groovy | 3 +-- main.nf | 2 +- modules.json | 22 ++++++---------------- nextflow_schema.json | 3 ++- workflows/sra.nf | 20 ++++++++++---------- 5 files changed, 20 insertions(+), 30 deletions(-) diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 9276512a..3d513a92 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -110,8 +110,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir" ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() diff --git a/main.nf b/main.nf index 1d849bd3..b600e82f 100644 --- a/main.nf +++ b/main.nf @@ -23,7 +23,7 @@ include { validateParameters; paramsHelp } from 'plugin/nf-validation' if (params.help) { def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + 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) } diff --git a/modules.json b/modules.json index 2daacf3a..3137b88b 100644 --- a/modules.json +++ b/modules.json @@ -8,30 +8,22 @@ "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/fasterqdump": { "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", - "installed_by": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "sratools/prefetch": { "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", - "installed_by": [ - "fastq_download_prefetch_fasterqdump_sratools" - ] + "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] } } }, @@ -40,12 +32,10 @@ "fastq_download_prefetch_fasterqdump_sratools": { "branch": "master", "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/nextflow_schema.json b/nextflow_schema.json index def56011..cda974a5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -69,7 +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", diff --git a/workflows/sra.nf b/workflows/sra.nf index 44ff8346..3a4809b6 100644 --- a/workflows/sra.nf +++ b/workflows/sra.nf @@ -4,14 +4,14 @@ ======================================================================================== */ -def valid_params = [ - ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5'] -] +include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation' -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// Validate input parameters -WorkflowSra.initialise(params, valid_params) +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation /* ======================================================================================== @@ -84,9 +84,9 @@ workflow SRA { if (!params.skip_fastq_download) { ch_sra_metadata - .map { - meta -> - [ meta, [ meta.fastq_1, meta.fastq_2 ] ] + .map { + meta -> + [ meta, [ meta.fastq_1, meta.fastq_2 ] ] } .branch { ftp: it[0].fastq_1 && !params.force_sratools_download @@ -115,7 +115,7 @@ workflow SRA { .out .fastq .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads) - .map { + .map { meta, fastq -> def reads = fastq instanceof List ? fastq.flatten() : [ fastq ] def meta_clone = meta.clone() From 71f6c3ceddbe6f612d62ed01f9f90b53254103b2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 14:33:05 +0200 Subject: [PATCH 5/8] update module --- modules.json | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules.json b/modules.json index 3137b88b..ab610dfb 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions From 52517c6cfa8e4cca0d87650e7abeb6884438b43f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 14:33:24 +0200 Subject: [PATCH 6/8] fix issue --- nextflow_schema.json | 1 - workflows/sra.nf | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index cda974a5..345601b7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -18,7 +18,6 @@ "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.(csv|tsv|txt)$", - "schema": "assets/schema_input.json", "fa_icon": "fas fa-file-excel", "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files." }, diff --git a/workflows/sra.nf b/workflows/sra.nf index 3a4809b6..8d396ca1 100644 --- a/workflows/sra.nf +++ b/workflows/sra.nf @@ -4,7 +4,7 @@ ======================================================================================== */ -include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation' +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' From f51446845daaee19d9489f8a6f24191fc6b3ce2d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 15:03:45 +0200 Subject: [PATCH 7/8] fix nf-validation issue --- assets/schema_input.json | 12 +++++++----- nextflow_schema.json | 1 + 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 9a800216..13044b1b 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -5,11 +5,13 @@ "description": "Schema for the file provided with params.input", "type": "array", "items": { - "type": "array", - "items": { - "type": "string", - "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$", - "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier" + "type": "object", + "properties": { + "": { + "type": "string", + "pattern": "^(((SR|ER|DR)[APRSX])|(SAM(N|EA|D))|(PRJ(NA|EB|DB))|(GS[EM])|(syn))(\\d+)$", + "errorMessage": "Please provide a valid SRA, ENA, DDBJ or GEO identifier" + } } } } diff --git a/nextflow_schema.json b/nextflow_schema.json index 345601b7..cda974a5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -18,6 +18,7 @@ "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.(csv|tsv|txt)$", + "schema": "assets/schema_input.json", "fa_icon": "fas fa-file-excel", "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files." }, From c3ed8e4439b8c65794aa397d820ce9becf507fd8 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 15:08:34 +0200 Subject: [PATCH 8/8] it's actually an id --- assets/schema_input.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 13044b1b..d451f9e9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -7,7 +7,7 @@ "items": { "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"