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nf-core/eager: [2.3.5] - Aalen (Patch) - 2021-06-04

James A. Fellows Yates; Alexander Peltzer; Thiseas C. Lamnidis; Maxime Borry; ZandraFagernas; Ido Bar; Aida Andrades Valtueña; alexandregilardet; nf-core bot; Maxime U. Garcia; Evan Floden; Phil Ewels; Patrick Hüther; Charles Plessy; Gisela Gabernet; sc13-bioinf; Åshild J. Vågene; Harshil Patel; Olga Botvinnik; Selina Carlhoff; Alex Hübner


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&lt;ul&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/722"&gt;#722&lt;/a&gt; - Adds bwa &lt;code&gt;-o&lt;/code&gt; flag for more flexibility in bwa parameters&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/736"&gt;#736&lt;/a&gt; - Add printing of multiqc run report location on successful completion&lt;/li&gt;
&lt;li&gt;New logo that is more visible when a user is using darkmode on GitHub or nf-core website!&lt;/li&gt;
&lt;/ul&gt;
&lt;code&gt;Fixed&lt;/code&gt;
&lt;ul&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/723"&gt;#723&lt;/a&gt; - Fixes empty fields in TSV resulting in uninformative error&lt;/li&gt;
&lt;li&gt;Updated template to nf-core/tools 1.14&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/688"&gt;#688&lt;/a&gt; - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/751"&gt;#751&lt;/a&gt; - Added missing label to mtnucratio&lt;/li&gt;
&lt;li&gt;General code cleanup and standardisation of parameters with no default setting&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/750"&gt;#750&lt;/a&gt; - Fixed piped commands requesting the same number of CPUs at each command step&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/757"&gt;#757&lt;/a&gt; - Removed confusing 'Data Type' variable from MultiQC workflow summary (not consistent with TSV input)&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/759"&gt;#759&lt;/a&gt; - Fixed malformed software scraping regex that resulted in N/A in MultiQC report&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/759"&gt;#761&lt;/a&gt; - Fixed issues related to instability of samtools filtering related CI tests&lt;/li&gt;
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