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nf-core/eager: [2.3.2] - Aalen (Patch) - 2021-01-14

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


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    <subfield code="a">&lt;code&gt;Added&lt;/code&gt;
&lt;ul&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/687"&gt;#687&lt;/a&gt; - Adds Kraken2 unique kmer counting report&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/676"&gt;#676&lt;/a&gt; - Refactor help message / summary message formatting to automatic versions using nf-core library&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/682"&gt;#682&lt;/a&gt; - Add AdapterRemoval &lt;code&gt;--qualitymax&lt;/code&gt; flag to allow FASTQ Phred score range max more than 41&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/666"&gt;#666&lt;/a&gt; - Fixed input file staging for &lt;code&gt;print_nuclear_contamination&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/631"&gt;#631&lt;/a&gt; - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled&lt;/li&gt;
&lt;li&gt;Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/652"&gt;#652&lt;/a&gt; - Added note to documentation that when using &lt;code&gt;--skip_collapse&lt;/code&gt; this will use &lt;em&gt;paired-end&lt;/em&gt; alignment mode with mappers when using PE data&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/626"&gt;#626&lt;/a&gt; - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty&lt;/li&gt;
&lt;li&gt;Added note to documentation that when using &lt;code&gt;--skip_collapse&lt;/code&gt; this will use &lt;em&gt;paired-end&lt;/em&gt; alignment mode with mappers when using PE data&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/673"&gt;#673&lt;/a&gt; - Fix Kraken database loading when loading from directory instead of compressed file&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/668"&gt;#688&lt;/a&gt; - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/683"&gt;#683&lt;/a&gt; - Sets &lt;code&gt;--igenomes_ignore&lt;/code&gt; to true by default, as rarely used by users currently and makes resolving configs less complex&lt;/li&gt;
&lt;li&gt;Added exit code &lt;code&gt;140&lt;/code&gt; to re-tryable exit code list to account for certain scheduler wall-time limit fails&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/672"&gt;#672&lt;/a&gt; - Removed java parameter from picard tools which could cause memory issues&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/679"&gt;#679&lt;/a&gt; - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/pull/690"&gt;#690&lt;/a&gt; - Fixed ANGSD output mode for beagle by setting &lt;code&gt;-doMajorMinor 1&lt;/code&gt; as default in that case&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/693"&gt;#693&lt;/a&gt; - Fixed broken TSV input validation for the Colour Chemistry column&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/695"&gt;#695&lt;/a&gt; - Fixed incorrect &lt;code&gt;-profile&lt;/code&gt; order in tutorials (originally written reversed due to &lt;a href="https://github.com/nextflow-io/nextflow/issues/1792"&gt;nextflow bug&lt;/a&gt;)&lt;/li&gt;
&lt;li&gt;&lt;a href="https://github.com/nf-core/eager/issues/653"&gt;#653&lt;/a&gt; - Fixed file collision errors with sexdeterrmine for two same-named libraries with different strandedness&lt;/li&gt;
&lt;/ul&gt;
&lt;code&gt;Dependencies&lt;/code&gt;
&lt;ul&gt;
&lt;li&gt;Bumped MultiQC to 1.10 for improved functionality&lt;/li&gt;
&lt;li&gt;Bumped HOPS to 0.35 for MultiQC 1.10 compatibility&lt;/li&gt;
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