From 42927e052d70d752f56e27ac2e25357ef707b8ca Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:13:55 +0000 Subject: [PATCH 01/12] 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-mhcquant_logo_light.png | Bin 10923 -> 72389 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowMain.groovy | 37 -- lib/WorkflowMhcquant.groovy | 45 +- main.nf | 16 + nextflow.config | 54 ++- nextflow_schema.json | 36 +- workflows/mhcquant.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 5ab7fd29..85b8f2be 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 cc533f97..7b4e5554 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 be94bacc..31969965 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/mhcquant/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ 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 b0e2d6a9..5b9fa054 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/mhcquant/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/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 20ce3a06..0d85ee51 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 6bdadbca..8c796490 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). -## v2.4.1dev - [date] +## v2.4.2dev - [date] Initial release of nf-core/mhcquant, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index f19ab2c2..294b745d 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 87585fa4..91f6fdec 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/mhcquant/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/mhcquant \ > 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/mhcquant/usage) and the [parameter documentation](https://nf-co.re/mhcquant/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/mhcquant/usage) and the [parameter documentation](https://nf-co.re/mhcquant/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/mhcquant/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/mhcquant/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/mhcquant/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index b2491dd8..11161424 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/mhcquant Methods Description" section_href: "https://github.com/nf-core/mhcquant" 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/mhcquant v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/mhcquant 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 43bfdcf6..09392396 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/mhcquant + This report has been generated by the nf-core/mhcquant analysis pipeline. 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with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index c6f3250c..0158c321 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 3a4a1543..e7a4bc6e 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/mhcquant --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/mhcquant --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/mhcquant -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("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 76b4668e..071d1c24 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${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/lib/WorkflowMhcquant.groovy b/lib/WorkflowMhcquant.groovy index 044727c5..6a90d5ab 100755 --- a/lib/WorkflowMhcquant.groovy +++ b/lib/WorkflowMhcquant.groovy @@ -11,6 +11,7 @@ class WorkflowMhcquant { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowMhcquant { 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/main.nf b/main.nf index 228e81a3..5ef5cf6e 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 ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index 7e142d3c..0839736c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${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/mhcquant profiles: ${params.custom_config_base}/pipeline/mhcquant.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_${trace_timestamp}.html" } manifest { @@ -219,8 +227,8 @@ manifest { homePage = 'https://github.com/nf-core/mhcquant' description = """Identify and quantify peptides from mass spectrometry raw data""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '2.4.1dev' + nextflowVersion = '!>=23.04.0' + version = '2.4.2dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 395dcc1f..180e3ac2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "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/mhcquant/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/mhcquant.nf b/workflows/mhcquant.nf index 069a32a9..a02bf0a1 100644 --- a/workflows/mhcquant.nf +++ b/workflows/mhcquant.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 -WorkflowMhcquant.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!' } +WorkflowMhcquant.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow MHCQUANT { // 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 MHCQUANT { workflow_summary = WorkflowMhcquant.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowMhcquant.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowMhcquant.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 14b71c234cf305c9ea6b1bad36dfd0d73520fedd Mon Sep 17 00:00:00 2001 From: Jonas Scheid Date: Wed, 19 Jul 2023 14:42:47 +0200 Subject: [PATCH 02/12] add loading modules.conf again --- conf/modules.config | 3 +-- nextflow.config | 4 +++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index dafddb66..150e20e9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -16,7 +16,6 @@ process { path: {"${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}"}, mode: params.publish_dir_mode, saveAs: {filename -> filename.equals('versions.yml') ? null : filename}, - enabled: false ] withName: 'SAMPLESHEET_CHECK' { @@ -164,7 +163,7 @@ process { withName: 'OPENMS_TEXTEXPORTER_UNQUANTIFIED|OPENMS_TEXTEXPORTER_QUANTIFIED' { publishDir = [ - path: {"${params.outdir}"}, + path: {"${params.outdir}/"}, mode: params.publish_dir_mode, pattern: '*.tsv' ] diff --git a/nextflow.config b/nextflow.config index 1bc5f4f9..d1274395 100644 --- a/nextflow.config +++ b/nextflow.config @@ -85,7 +85,6 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null publish_dir_mode = 'copy' email = null email_on_fail = null @@ -285,6 +284,9 @@ manifest { doi = '' } +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + // Function to ensure that resource requirements don't go beyond // a maximum limit def check_max(obj, type) { From c7bc5bd1f245611dc13a89e5eb767db375b54409 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 14:48:07 +0200 Subject: [PATCH 03/12] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 04f64f02..18a6bc0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Made file extension check case insensitive - Added option to provide a default comet parameters file - Optimize resource allocations +- Template update 2.9. [#274](https://github.com/nf-core/mhcquant/pull/274) ### `Fixed` From e147260631cb509178b39591155531ad2b488a5c Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 14:51:56 +0200 Subject: [PATCH 04/12] fix nextflow version for fulltest --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9776f2c3..ed2d9d2e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,7 +49,7 @@ jobs: # Nextflow versions include: # Test pipeline minimum Nextflow version - - NXF_VER: "22.10.1" + - NXF_VER: "23.04.0" NXF_EDGE: "" # Test latest edge release of Nextflow - NXF_VER: "" From 15f94ef8e8b70314441f543bd473710071f14c7a Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 14:56:18 +0200 Subject: [PATCH 05/12] fix gh ci for fulltest --- .github/workflows/ci.yml | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ed2d9d2e..fc50856a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,27 +46,17 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - # Nextflow versions - include: - # Test pipeline minimum Nextflow version - - NXF_VER: "23.04.0" - NXF_EDGE: "" - # Test latest edge release of Nextflow - - NXF_VER: "" - NXF_EDGE: "1" + NXF_VER: + - "23.04.0" + - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Install Nextflow - env: - NXF_VER: ${{ matrix.NXF_VER }} - # Uncomment only if the edge release is more recent than the latest stable release - # See https://github.com/nextflow-io/nextflow/issues/2467 - # NXF_EDGE: ${{ matrix.NXF_EDGE }} - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Run pipeline with additional params run: | From 621fdeba7854c6d384492e1503c20da0d948799d Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 15:27:07 +0200 Subject: [PATCH 06/12] add novel params to fulltest --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fc50856a..822c1c48 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -60,4 +60,4 @@ jobs: - name: Run pipeline with additional params run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --use_deeplc --use_ms2pip --outdir ./results From b1a7fb4fd2141eeda921bdd81b1887128da16294 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 15:27:31 +0200 Subject: [PATCH 07/12] fix old conda implementation in modules --- modules/local/generate_proteins_from_vcf.nf | 2 +- modules/local/mhcflurry_predictneoepitopesclass1.nf | 2 +- modules/local/mhcflurry_predictpeptidesclass1.nf | 2 +- modules/local/mhcflurry_predictpsms.nf | 2 +- modules/local/mhcnuggets_neoepitopesclass2post.nf | 2 +- modules/local/mhcnuggets_neoepitopesclass2pre.nf | 2 +- modules/local/mhcnuggets_peptidesclass2post.nf | 2 +- modules/local/mhcnuggets_peptidesclass2pre.nf | 2 +- modules/local/mhcnuggets_predictneoepitopesclass2.nf | 2 +- modules/local/mhcnuggets_predictpeptidesclass2.nf | 2 +- modules/local/openms_cometadapter.nf | 2 +- modules/local/openms_decoydatabase.nf | 2 +- modules/local/openms_falsediscoveryrate.nf | 2 +- modules/local/openms_featurefinderidentification.nf | 2 +- modules/local/openms_featurelinkerunlabeledkd.nf | 2 +- modules/local/openms_filefilter.nf | 2 +- modules/local/openms_idconflictresolver.nf | 2 +- modules/local/openms_idfilter.nf | 2 +- modules/local/openms_idmerger.nf | 2 +- modules/local/openms_mapaligneridentification.nf | 2 +- modules/local/openms_maprttransformer.nf | 2 +- modules/local/openms_mztabexporter.nf | 2 +- modules/local/openms_peakpickerhires.nf | 2 +- modules/local/openms_peptideindexer.nf | 2 +- modules/local/openms_percolatoradapter.nf | 2 +- modules/local/openms_psmfeatureextractor.nf | 2 +- modules/local/openms_rtmodel.nf | 2 +- modules/local/openms_rtpredict.nf | 2 +- modules/local/openms_textexporter.nf | 2 +- modules/local/predict_possible_neoepitopes.nf | 2 +- modules/local/pyopenms_ionannotator.nf | 2 +- modules/local/resolve_found_neoepitopes.nf | 2 +- modules/local/thermorawfileparser.nf | 2 +- 33 files changed, 33 insertions(+), 33 deletions(-) diff --git a/modules/local/generate_proteins_from_vcf.nf b/modules/local/generate_proteins_from_vcf.nf index 09c6db8a..d91e5384 100644 --- a/modules/local/generate_proteins_from_vcf.nf +++ b/modules/local/generate_proteins_from_vcf.nf @@ -2,7 +2,7 @@ process GENERATE_PROTEINS_FROM_VCF { tag "$meta" label 'process_medium' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/mhcflurry_predictneoepitopesclass1.nf b/modules/local/mhcflurry_predictneoepitopesclass1.nf index 003bf043..f0b72fd2 100644 --- a/modules/local/mhcflurry_predictneoepitopesclass1.nf +++ b/modules/local/mhcflurry_predictneoepitopesclass1.nf @@ -2,7 +2,7 @@ process MHCFLURRY_PREDICTNEOEPITOPESCLASS1 { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/mhcflurry_predictpeptidesclass1.nf b/modules/local/mhcflurry_predictpeptidesclass1.nf index b7a0a42e..aa45acd3 100644 --- a/modules/local/mhcflurry_predictpeptidesclass1.nf +++ b/modules/local/mhcflurry_predictpeptidesclass1.nf @@ -2,7 +2,7 @@ process MHCFLURRY_PREDICTPEPTIDESCLASS1 { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/mhcflurry_predictpsms.nf b/modules/local/mhcflurry_predictpsms.nf index 22c5be03..87159089 100644 --- a/modules/local/mhcflurry_predictpsms.nf +++ b/modules/local/mhcflurry_predictpsms.nf @@ -2,7 +2,7 @@ process MHCFLURRY_PREDICTPSMS { tag "$meta" label 'process_medium' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/mhcnuggets_neoepitopesclass2post.nf b/modules/local/mhcnuggets_neoepitopesclass2post.nf index f97bf3e3..088a491a 100644 --- a/modules/local/mhcnuggets_neoepitopesclass2post.nf +++ b/modules/local/mhcnuggets_neoepitopesclass2post.nf @@ -2,7 +2,7 @@ process MHCNUGGETS_NEOEPITOPESCLASS2POST { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mhcnuggets:2.3.2--py_0' : 'biocontainers/mhcnuggets:2.3.2--py_0' }" diff --git a/modules/local/mhcnuggets_neoepitopesclass2pre.nf b/modules/local/mhcnuggets_neoepitopesclass2pre.nf index f459be9a..597970aa 100644 --- a/modules/local/mhcnuggets_neoepitopesclass2pre.nf +++ b/modules/local/mhcnuggets_neoepitopesclass2pre.nf @@ -2,7 +2,7 @@ process MHCNUGGETS_NEOEPITOPESCLASS2PRE { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mhcnuggets:2.3.2--py_0' : 'biocontainers/mhcnuggets:2.3.2--py_0' }" diff --git a/modules/local/mhcnuggets_peptidesclass2post.nf b/modules/local/mhcnuggets_peptidesclass2post.nf index 2a6e7323..fe94dc20 100644 --- a/modules/local/mhcnuggets_peptidesclass2post.nf +++ b/modules/local/mhcnuggets_peptidesclass2post.nf @@ -2,7 +2,7 @@ process MHCNUGGETS_PEPTIDESCLASS2POST { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mhcnuggets:2.3.2--py_0' : 'biocontainers/mhcnuggets:2.3.2--py_0' }" diff --git a/modules/local/mhcnuggets_peptidesclass2pre.nf b/modules/local/mhcnuggets_peptidesclass2pre.nf index 01a4d561..8f8a6a83 100644 --- a/modules/local/mhcnuggets_peptidesclass2pre.nf +++ b/modules/local/mhcnuggets_peptidesclass2pre.nf @@ -2,7 +2,7 @@ process MHCNUGGETS_PEPTIDESCLASS2PRE { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mhcnuggets:2.3.2--py_0' : 'biocontainers/mhcnuggets:2.3.2--py_0' }" diff --git a/modules/local/mhcnuggets_predictneoepitopesclass2.nf b/modules/local/mhcnuggets_predictneoepitopesclass2.nf index 1a6f5b3a..03b99d81 100644 --- a/modules/local/mhcnuggets_predictneoepitopesclass2.nf +++ b/modules/local/mhcnuggets_predictneoepitopesclass2.nf @@ -2,7 +2,7 @@ process MHCNUGGETS_PREDICTNEOEPITOPESCLASS2 { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/mhcnuggets_predictpeptidesclass2.nf b/modules/local/mhcnuggets_predictpeptidesclass2.nf index 4564e2b0..69364007 100644 --- a/modules/local/mhcnuggets_predictpeptidesclass2.nf +++ b/modules/local/mhcnuggets_predictpeptidesclass2.nf @@ -2,7 +2,7 @@ process MHCNUGGETS_PREDICTPEPTIDESCLASS2 { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/openms_cometadapter.nf b/modules/local/openms_cometadapter.nf index 4360ffab..ab531a9d 100644 --- a/modules/local/openms_cometadapter.nf +++ b/modules/local/openms_cometadapter.nf @@ -2,7 +2,7 @@ process OPENMS_COMETADAPTER { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::openms-thirdparty=2.8.0" : null) + conda "bioconda::openms-thirdparty=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.9.1--h9ee0642_1' : 'biocontainers/openms-thirdparty:2.9.1--h9ee0642_1' }" diff --git a/modules/local/openms_decoydatabase.nf b/modules/local/openms_decoydatabase.nf index 1de1b82e..3c4970d6 100644 --- a/modules/local/openms_decoydatabase.nf +++ b/modules/local/openms_decoydatabase.nf @@ -2,7 +2,7 @@ process OPENMS_DECOYDATABASE { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_falsediscoveryrate.nf b/modules/local/openms_falsediscoveryrate.nf index 0577c519..8ff40dd8 100644 --- a/modules/local/openms_falsediscoveryrate.nf +++ b/modules/local/openms_falsediscoveryrate.nf @@ -2,7 +2,7 @@ process OPENMS_FALSEDISCOVERYRATE { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_featurefinderidentification.nf b/modules/local/openms_featurefinderidentification.nf index 54cdc199..c4f3bd65 100644 --- a/modules/local/openms_featurefinderidentification.nf +++ b/modules/local/openms_featurefinderidentification.nf @@ -2,7 +2,7 @@ process OPENMS_FEATUREFINDERIDENTIFICATION { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_featurelinkerunlabeledkd.nf b/modules/local/openms_featurelinkerunlabeledkd.nf index 7c5f8409..e4976128 100644 --- a/modules/local/openms_featurelinkerunlabeledkd.nf +++ b/modules/local/openms_featurelinkerunlabeledkd.nf @@ -2,7 +2,7 @@ process OPENMS_FEATURELINKERUNLABELEDKD { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms-thirdparty=2.8.0" : null) + conda "bioconda::openms-thirdparty=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.9.1--h9ee0642_1' : 'biocontainers/openms-thirdparty:2.9.1--h9ee0642_1' }" diff --git a/modules/local/openms_filefilter.nf b/modules/local/openms_filefilter.nf index c366557c..27da384c 100644 --- a/modules/local/openms_filefilter.nf +++ b/modules/local/openms_filefilter.nf @@ -2,7 +2,7 @@ process OPENMS_FILEFILTER { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::openms=2.9.1" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_idconflictresolver.nf b/modules/local/openms_idconflictresolver.nf index c5f6b9c6..b089820a 100644 --- a/modules/local/openms_idconflictresolver.nf +++ b/modules/local/openms_idconflictresolver.nf @@ -2,7 +2,7 @@ process OPENMS_IDCONFLICTRESOLVER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_idfilter.nf b/modules/local/openms_idfilter.nf index a2c8ec28..9c807c15 100644 --- a/modules/local/openms_idfilter.nf +++ b/modules/local/openms_idfilter.nf @@ -2,7 +2,7 @@ process OPENMS_IDFILTER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_idmerger.nf b/modules/local/openms_idmerger.nf index f0dc150c..08db7778 100644 --- a/modules/local/openms_idmerger.nf +++ b/modules/local/openms_idmerger.nf @@ -2,7 +2,7 @@ process OPENMS_IDMERGER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_mapaligneridentification.nf b/modules/local/openms_mapaligneridentification.nf index aaa0efba..e4f0e91b 100644 --- a/modules/local/openms_mapaligneridentification.nf +++ b/modules/local/openms_mapaligneridentification.nf @@ -2,7 +2,7 @@ process OPENMS_MAPALIGNERIDENTIFICATION { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_maprttransformer.nf b/modules/local/openms_maprttransformer.nf index fda88260..0026990d 100644 --- a/modules/local/openms_maprttransformer.nf +++ b/modules/local/openms_maprttransformer.nf @@ -2,7 +2,7 @@ process OPENMS_MAPRTTRANSFORMER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_mztabexporter.nf b/modules/local/openms_mztabexporter.nf index 1c2072fa..f87aa53c 100644 --- a/modules/local/openms_mztabexporter.nf +++ b/modules/local/openms_mztabexporter.nf @@ -2,7 +2,7 @@ process OPENMS_MZTABEXPORTER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_peakpickerhires.nf b/modules/local/openms_peakpickerhires.nf index 0a7e2e9b..588ba8c3 100644 --- a/modules/local/openms_peakpickerhires.nf +++ b/modules/local/openms_peakpickerhires.nf @@ -2,7 +2,7 @@ process OPENMS_PEAKPICKERHIRES { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_peptideindexer.nf b/modules/local/openms_peptideindexer.nf index 3a576b20..d6dcc63b 100644 --- a/modules/local/openms_peptideindexer.nf +++ b/modules/local/openms_peptideindexer.nf @@ -2,7 +2,7 @@ process OPENMS_PEPTIDEINDEXER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_percolatoradapter.nf b/modules/local/openms_percolatoradapter.nf index 4f2a80d1..f2057d34 100644 --- a/modules/local/openms_percolatoradapter.nf +++ b/modules/local/openms_percolatoradapter.nf @@ -2,7 +2,7 @@ process OPENMS_PERCOLATORADAPTER { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::openms-thirdparty=2.8.0" : null) + conda "bioconda::openms-thirdparty=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.9.1--h9ee0642_1' : 'biocontainers/openms-thirdparty:2.9.1--h9ee0642_1' }" diff --git a/modules/local/openms_psmfeatureextractor.nf b/modules/local/openms_psmfeatureextractor.nf index 1d89a144..29e4fa24 100644 --- a/modules/local/openms_psmfeatureextractor.nf +++ b/modules/local/openms_psmfeatureextractor.nf @@ -2,7 +2,7 @@ process OPENMS_PSMFEATUREEXTRACTOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_rtmodel.nf b/modules/local/openms_rtmodel.nf index 021b21c0..5a9aa85a 100644 --- a/modules/local/openms_rtmodel.nf +++ b/modules/local/openms_rtmodel.nf @@ -2,7 +2,7 @@ process OPENMS_RTMODEL { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/openms_rtpredict.nf b/modules/local/openms_rtpredict.nf index 02b6e488..933823b0 100644 --- a/modules/local/openms_rtpredict.nf +++ b/modules/local/openms_rtpredict.nf @@ -2,7 +2,7 @@ process OPENMS_RTPREDICT { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms-thirdparty=2.8.0" : null) + conda "bioconda::openms-thirdparty=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.9.1--h9ee0642_1' : 'biocontainers/openms-thirdparty:2.9.1--h9ee0642_1' }" diff --git a/modules/local/openms_textexporter.nf b/modules/local/openms_textexporter.nf index be784040..09d53349 100644 --- a/modules/local/openms_textexporter.nf +++ b/modules/local/openms_textexporter.nf @@ -2,7 +2,7 @@ process OPENMS_TEXTEXPORTER { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "bioconda::openms=2.8.0" : null) + conda "bioconda::openms=2.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_1' : 'quay.io/biocontainers/openms:2.9.1--h135471a_1' }" diff --git a/modules/local/predict_possible_neoepitopes.nf b/modules/local/predict_possible_neoepitopes.nf index 614613b9..c469b469 100644 --- a/modules/local/predict_possible_neoepitopes.nf +++ b/modules/local/predict_possible_neoepitopes.nf @@ -2,7 +2,7 @@ process PREDICT_POSSIBLE_NEOEPITOPES { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/pyopenms_ionannotator.nf b/modules/local/pyopenms_ionannotator.nf index 7115d102..8fdb9f83 100644 --- a/modules/local/pyopenms_ionannotator.nf +++ b/modules/local/pyopenms_ionannotator.nf @@ -2,7 +2,7 @@ process PYOPENMS_IONANNOTATOR { tag "$sample" label 'process_high' - conda (params.enable_conda ? "bioconda::pyopenms=2.8.0" : null) + conda "bioconda::pyopenms=2.8.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pyopenms:2.8.0--py310h3dc0cdb_1' : 'biocontainers/pyopenms:2.8.0--py310h3dc0cdb_1' }" diff --git a/modules/local/resolve_found_neoepitopes.nf b/modules/local/resolve_found_neoepitopes.nf index 31fc64c8..4dce9107 100644 --- a/modules/local/resolve_found_neoepitopes.nf +++ b/modules/local/resolve_found_neoepitopes.nf @@ -2,7 +2,7 @@ process RESOLVE_FOUND_NEOEPITOPES { tag "$meta" label 'process_low' - conda (params.enable_conda ? "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" : null) + conda "bioconda::fred2=2.0.7 bioconda::mhcflurry=1.4.3 bioconda::mhcnuggets=2.3.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' : 'biocontainers/mulled-v2-c3f301504f7fa2e7bf81c3783de19a9990ea3001:12b1b9f040fd92a80629d58f8a558dde4820eb15-0' }" diff --git a/modules/local/thermorawfileparser.nf b/modules/local/thermorawfileparser.nf index 853b6ea1..8385a33c 100644 --- a/modules/local/thermorawfileparser.nf +++ b/modules/local/thermorawfileparser.nf @@ -2,7 +2,7 @@ process THERMORAWFILEPARSER { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::thermorawfileparser=1.4.2" : null) + conda "bioconda::thermorawfileparser=1.4.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/thermorawfileparser:1.4.2--ha8f3691_0' : 'biocontainers/thermorawfileparser:1.4.2--ha8f3691_0' }" From 7b88d9c5be6f71190c0ba599bfbaffd7d0310968 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 15:28:52 +0200 Subject: [PATCH 08/12] adjust authors --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index d1274395..3174ff6c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -275,7 +275,7 @@ dag { manifest { name = 'nf-core/mhcquant' - author = """Leon Bichmann, Marissa Dubbelaar""" + author = """Leon Bichmann, Marissa Dubbelaar, Jonas Scheid, Steffen Lemke""" homePage = 'https://github.com/nf-core/mhcquant' description = """Identify and quantify peptides from mass spectrometry raw data""" mainScript = 'main.nf' From 706538d0b31d75735efa60729ca41c4e65665186 Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 15:29:33 +0200 Subject: [PATCH 09/12] remove fastqc from citations --- CITATIONS.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 31a3fd3c..a9df5143 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -26,9 +26,6 @@ > Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walze M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624 -- [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/) From 9ac8f457ec1f8f18e543feef39e7f6476584eeae Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 15:35:52 +0200 Subject: [PATCH 10/12] prettier --- CITATIONS.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index a9df5143..64807a32 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -26,7 +26,6 @@ > Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walze M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624 - - [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. From 516f05430e7fbdf1eeb6bc1198d60c3d91ed60ff Mon Sep 17 00:00:00 2001 From: jonasscheid Date: Wed, 19 Jul 2023 15:41:36 +0200 Subject: [PATCH 11/12] adjust license --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index 43eea689..fa6e5d35 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Leon Bichmann, Marissa Dubbelaar +Copyright (c) Leon Bichmann, Marissa Dubbelaar, Jonas Scheid, Steffen Lemke Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From 795ec22700fd2f01d60c7b3f7182707ad2817f5f Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Thu, 20 Jul 2023 13:29:06 +0200 Subject: [PATCH 12/12] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 3174ff6c..702fb6c3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -281,7 +281,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '2.4.2dev' - doi = '' + doi = '10.1021/acs.jproteome.9b00313' } // Load modules.config for DSL2 module specific options