Template update for nf-core/tools version 2.6
nf-core-bot
2 years ago
parent
28045430d1
commit
51bacb00e6
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{
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"type": "message",
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"attachments": [
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{
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"contentType": "application/vnd.microsoft.card.adaptive",
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"contentUrl": null,
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"content": {
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"\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
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"msteams": {
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"width": "Full"
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},
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"type": "AdaptiveCard",
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"version": "1.2",
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"body": [
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{
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"type": "TextBlock",
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"size": "Large",
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"weight": "Bolder",
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"color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
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"text": "nf-core/taxprofiler v${version} - ${runName}",
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"wrap": true
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},
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{
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"type": "TextBlock",
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"spacing": "None",
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"text": "Completed at ${dateComplete} (duration: ${duration})",
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"isSubtle": true,
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"wrap": true
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},
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{
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"type": "TextBlock",
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"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
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"wrap": true
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},
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{
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"type": "TextBlock",
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"text": "The command used to launch the workflow was as follows:",
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"wrap": true
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},
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{
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"type": "TextBlock",
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"text": "${commandLine}",
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"isSubtle": true,
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"wrap": true
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}
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],
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"actions": [
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{
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"type": "Action.ShowCard",
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"title": "Pipeline Configuration",
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"card": {
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"type": "AdaptiveCard",
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"\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
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"body": [
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{
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"type": "FactSet",
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"facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
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]
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}
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]
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}
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}
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]
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}
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}
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]
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}
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id: "nf-core-taxprofiler-methods-description"
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description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
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section_name: "nf-core/taxprofiler Methods Description"
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section_href: "https://github.com/nf-core/taxprofiler"
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plot_type: "html"
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## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
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## You inject any metadata in the Nextflow '${workflow}' object
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data: |
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<h4>Methods</h4>
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<p>Data was processed using nf-core/taxprofiler v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
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<p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
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<pre><code>${workflow.commandLine}</code></pre>
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<h4>References</h4>
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<ul>
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<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
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<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
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</ul>
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<div class="alert alert-info">
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<h5>Notes:</h5>
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<ul>
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${nodoi_text}
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<li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
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<li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
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</ul>
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</div>
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@ -1,11 +1,11 @@
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process CUSTOM_DUMPSOFTWAREVERSIONS {
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label 'process_low'
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label 'process_single'
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// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
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conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
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conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
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input:
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path versions
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@ -1,31 +0,0 @@
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process MULTIQC {
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
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input:
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path multiqc_files
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output:
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path "*multiqc_report.html", emit: report
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path "*_data" , emit: data
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path "*_plots" , optional:true, emit: plots
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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multiqc -f $args .
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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END_VERSIONS
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"""
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}
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@ -0,0 +1,53 @@
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process MULTIQC {
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label 'process_single'
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conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
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input:
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path multiqc_files, stageAs: "?/*"
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path(multiqc_config)
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path(extra_multiqc_config)
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path(multiqc_logo)
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output:
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path "*multiqc_report.html", emit: report
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path "*_data" , emit: data
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path "*_plots" , optional:true, emit: plots
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def config = multiqc_config ? "--config $multiqc_config" : ''
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def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
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"""
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multiqc \\
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--force \\
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$args \\
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$config \\
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$extra_config \\
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.
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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END_VERSIONS
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"""
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stub:
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"""
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touch multiqc_data
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touch multiqc_plots
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touch multiqc_report.html
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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END_VERSIONS
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"""
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}
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