From 2bfd1d715dd51e3bb81fe9f2dbb7c16b1fa33260 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 17 Oct 2024 07:24:09 +0000 Subject: [PATCH] Template update for nf-core/tools version 3.0.2 --- .github/CONTRIBUTING.md | 2 - .nf-core.yml | 3 +- CHANGELOG.md | 2 +- CITATIONS.md | 4 - README.md | 2 - assets/methods_description_template.yml | 29 ------ assets/multiqc_config.yml | 15 --- assets/sendmail_template.txt | 22 ----- conf/modules.config | 8 -- docs/output.md | 19 +--- docs/usage.md | 2 +- main.nf | 4 +- modules.json | 8 +- modules/nf-core/multiqc/environment.yml | 5 - modules/nf-core/multiqc/main.nf | 63 ------------- modules/nf-core/multiqc/meta.yml | 78 ---------------- modules/nf-core/multiqc/tests/main.nf.test | 92 ------------------- .../nf-core/multiqc/tests/main.nf.test.snap | 41 --------- modules/nf-core/multiqc/tests/nextflow.config | 5 - modules/nf-core/multiqc/tests/tags.yml | 2 - nextflow.config | 9 +- nextflow_schema.json | 31 ------- .../utils_nfcore_tfactivity_pipeline/main.nf | 8 +- tower.yml | 2 - workflows/tfactivity.nf | 50 +--------- 25 files changed, 18 insertions(+), 488 deletions(-) delete mode 100644 assets/methods_description_template.yml delete mode 100644 assets/multiqc_config.yml delete mode 100644 modules/nf-core/multiqc/environment.yml delete mode 100644 modules/nf-core/multiqc/main.nf delete mode 100644 modules/nf-core/multiqc/meta.yml delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap delete mode 100644 modules/nf-core/multiqc/tests/nextflow.config delete mode 100644 modules/nf-core/multiqc/tests/tags.yml diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 421bb1b..798208c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -79,8 +79,6 @@ If you wish to contribute a new step, please use the following coding standards: 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. -9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. -10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. ### Default values diff --git a/.nf-core.yml b/.nf-core.yml index 031525c..f7ae1ff 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -21,5 +21,6 @@ template: outdir: . skip_features: - fastqc - version: 1.0dev + - multiqc + version: 0.0.1dev update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index e696753..f78d291 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). -## v1.0dev - [date] +## v0.0.1dev - [date] Initial release of nf-core/tfactivity, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index e3228a5..8873e2d 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,10 +10,6 @@ ## Pipeline tools -- [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 - [Anaconda](https://anaconda.com) diff --git a/README.md b/README.md index 46ddd14..53237e3 100644 --- a/README.md +++ b/README.md @@ -31,8 +31,6 @@ workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. --> -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) - ## Usage > [!NOTE] diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml deleted file mode 100644 index 909d03c..0000000 --- a/assets/methods_description_template.yml +++ /dev/null @@ -1,29 +0,0 @@ -id: "nf-core-tfactivity-methods-description" -description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "nf-core/tfactivity Methods Description" -section_href: "https://github.com/nf-core/tfactivity" -plot_type: "html" -## 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/tfactivity 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 deleted file mode 100644 index 99b5260..0000000 --- a/assets/multiqc_config.yml +++ /dev/null @@ -1,15 +0,0 @@ -report_comment: > - This report has been generated by the nf-core/tfactivity - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - "nf-core-tfactivity-methods-description": - order: -1000 - software_versions: - order: -1001 - "nf-core-tfactivity-summary": - order: -1002 - -export_plots: true - -disable_version_detection: true diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index b5a7cc0..24143e4 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -26,28 +26,6 @@ Content-Disposition: inline; filename="nf-core-tfactivity_logo_light.png" join( '\n' ) %> <% -if (mqcFile){ -def mqcFileObj = new File("$mqcFile") -if (mqcFileObj.length() < mqcMaxSize){ -out << """ ---nfcoremimeboundary -Content-Type: text/html; name=\"multiqc_report\" -Content-Transfer-Encoding: base64 -Content-ID: -Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" - -${mqcFileObj. - bytes. - encodeBase64(). - toString(). - tokenize( '\n' )*. - toList()*. - collate( 76 )*. - collect { it.join() }. - flatten(). - join( '\n' )} -""" -}} %> --nfcoremimeboundary-- diff --git a/conf/modules.config b/conf/modules.config index 255b138..3ca9a37 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -19,13 +19,5 @@ process { ] - withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } - publishDir = [ - path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } diff --git a/docs/output.md b/docs/output.md index a62be0f..0c9948c 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,7 +2,7 @@ ## Introduction -This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. +This document describes the output produced by the pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. @@ -12,25 +12,8 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution -### MultiQC - -
-Output files - -- `multiqc/` - - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - - `multiqc_plots/`: directory containing static images from the report in various formats. - -
- -[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. - -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . - ### Pipeline information
diff --git a/docs/usage.md b/docs/usage.md index d84879b..39992a3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -110,7 +110,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you First, go to the [nf-core/tfactivity releases page](https://github.com/nf-core/tfactivity/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. diff --git a/main.nf b/main.nf index 06b7ebb..7c4c357 100644 --- a/main.nf +++ b/main.nf @@ -53,8 +53,6 @@ workflow NFCORE_TFACTIVITY { TFACTIVITY ( samplesheet ) - emit: - multiqc_report = TFACTIVITY.out.multiqc_report // channel: /path/to/multiqc_report.html } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -93,7 +91,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - NFCORE_TFACTIVITY.out.multiqc_report + ) } diff --git a/modules.json b/modules.json index d9e4b4a..2a13478 100644 --- a/modules.json +++ b/modules.json @@ -4,13 +4,7 @@ "repos": { "https://github.com/nf-core/modules.git": { "modules": { - "nf-core": { - "multiqc": { - "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] - } - } + "nf-core": {} }, "subworkflows": { "nf-core": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml deleted file mode 100644 index 6f5b867..0000000 --- a/modules/nf-core/multiqc/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf deleted file mode 100644 index cc0643e..0000000 --- a/modules/nf-core/multiqc/main.nf +++ /dev/null @@ -1,63 +0,0 @@ -process MULTIQC { - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" - - input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - path(replace_names) - path(sample_names) - - output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' - def replace = replace_names ? "--replace-names ${replace_names}" : '' - def samples = sample_names ? "--sample-names ${sample_names}" : '' - """ - multiqc \\ - --force \\ - $args \\ - $config \\ - $prefix \\ - $extra_config \\ - $logo \\ - $replace \\ - $samples \\ - . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ - - stub: - """ - mkdir multiqc_data - mkdir multiqc_plots - touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml deleted file mode 100644 index b16c187..0000000 --- a/modules/nf-core/multiqc/meta.yml +++ /dev/null @@ -1,78 +0,0 @@ -name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into - a single report -keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report -tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] - identifier: biotools:multiqc -input: - - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections - in multiqc_config. - pattern: "*.{yml,yaml}" - - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" -output: - - report: - - "*multiqc_report.html": - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - - "*_data": - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - - "*_plots": - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" -maintainers: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test deleted file mode 100644 index 33316a7..0000000 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ /dev/null @@ -1,92 +0,0 @@ -nextflow_process { - - name "Test Process MULTIQC" - script "../main.nf" - process "MULTIQC" - - tag "modules" - tag "modules_nfcore" - tag "multiqc" - - config "./nextflow.config" - - test("sarscov2 single-end [fastqc]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) - } - - } - - test("sarscov2 single-end [fastqc] [config]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) - } - } - - test("sarscov2 single-end [fastqc] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } - ) - } - - } -} diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap deleted file mode 100644 index 2fcbb5f..0000000 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ /dev/null @@ -1,41 +0,0 @@ -{ - "multiqc_versions_single": { - "content": [ - [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T17:51:46.317523" - }, - "multiqc_stub": { - "content": [ - [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T17:52:20.680978" - }, - "multiqc_versions_config": { - "content": [ - [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-02T17:52:09.185842" - } -} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config deleted file mode 100644 index c537a6a..0000000 --- a/modules/nf-core/multiqc/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: 'MULTIQC' { - ext.prefix = null - } -} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index f50e542..fc58da8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -18,12 +18,7 @@ params { igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - // 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 @@ -226,7 +221,7 @@ manifest { description = """TBD""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '1.0dev' + version = '0.0.1dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 407dfb6..11a9839 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -35,11 +35,6 @@ "fa_icon": "fas fa-envelope", "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" - }, - "multiqc_title": { - "type": "string", - "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", - "fa_icon": "fas fa-file-signature" } } }, @@ -166,14 +161,6 @@ "fa_icon": "fas fa-remove-format", "hidden": true }, - "max_multiqc_email_size": { - "type": "string", - "description": "File size limit when attaching MultiQC reports to summary emails.", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "default": "25.MB", - "fa_icon": "fas fa-file-upload", - "hidden": true - }, "monochrome_logs": { "type": "boolean", "description": "Do not use coloured log outputs.", @@ -187,24 +174,6 @@ "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", diff --git a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf index a8bfad6..ba4afcc 100644 --- a/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_tfactivity_pipeline/main.nf @@ -112,7 +112,7 @@ workflow PIPELINE_COMPLETION { outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications - multiqc_report // string: Path to MultiQC report + main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") @@ -129,7 +129,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_report.toList() + [] ) } @@ -205,7 +205,7 @@ def toolCitationText() { def citation_text = [ "Tools used in the workflow included:", - "MultiQC (Ewels et al. 2016)", + "." ].join(' ').trim() @@ -218,7 +218,7 @@ def toolBibliographyText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ - "
  • 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 diff --git a/tower.yml b/tower.yml index 787aedf..c61323c 100644 --- a/tower.yml +++ b/tower.yml @@ -1,5 +1,3 @@ reports: - multiqc_report.html: - display: "MultiQC HTML report" samplesheet.csv: display: "Auto-created samplesheet with collated metadata and FASTQ paths" diff --git a/workflows/tfactivity.nf b/workflows/tfactivity.nf index a0b34af..fd373b6 100644 --- a/workflows/tfactivity.nf +++ b/workflows/tfactivity.nf @@ -4,9 +4,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { MULTIQC } from '../modules/nf-core/multiqc/main' + include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' + include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_tfactivity_pipeline' @@ -23,7 +23,7 @@ workflow TFACTIVITY { main: ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() + // // Collate and save software versions @@ -31,53 +31,13 @@ workflow TFACTIVITY { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', + name: 'nf_core_' + 'pipeline_software_' + '' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } - // - // MODULE: MultiQC - // - ch_multiqc_config = Channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? - file(params.multiqc_methods_description, checkIfExists: true) : - file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value( - methodsDescriptionText(ch_multiqc_custom_methods_description)) - - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix( - ch_methods_description.collectFile( - name: 'methods_description_mqc.yaml', - sort: true - ) - ) - - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), - [], - [] - ) - - emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit: versions = ch_versions // channel: [ path(versions.yml) ] }