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Fix bracket in wrong place
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assets/methods_description_template.yml

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@@ -7,7 +7,7 @@ plot_type: "html"
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## You inject any metadata in the Nextflow '${workflow}' object
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data: |
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<h4>Methods</h4>
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<p>Data was processed using nf-core/mag v${workflow.manifest.version} (${doi_text; <a href="https://doi.org/10.1093/nargab/lqac007">Krakau <em>et al.</em>, 2022</a>)} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
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<p>Data was processed using nf-core/mag v${workflow.manifest.version} (${doi_text}; <a href="https://doi.org/10.1093/nargab/lqac007">Krakau <em>et al.</em>, 2022</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
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<p>The pipeline was executed with Nextflow v${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>${workflow.commandLine}</code></pre>
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<p>${tool_citations}</p>

lib/WorkflowMag.groovy

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@@ -10,7 +10,7 @@ class WorkflowMag {
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//
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// Check and validate parameters
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//
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public static void initialise(params, log, hybrid) {
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// Check if binning mapping mode is valid
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if (!['all', 'group', 'own'].contains(params.binning_map_mode)) {
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// Pipeline DOI
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meta["doi_text"] = meta.manifest_map.doi ? "(doi: <a href=\'https://doi.org/${meta.manifest_map.doi}\'>${meta.manifest_map.doi}</a>)" : ""
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meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
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meta["nodoi_text"] = meta.manifest_map.doi ? "" : "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
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// Tool references
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meta["tool_citations"] = ""

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