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