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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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  <dc:creator>James A. Fellows Yates</dc:creator>
  <dc:creator>Alexander Peltzer</dc:creator>
  <dc:creator>Thiseas C. Lamnidis</dc:creator>
  <dc:creator>Maxime Borry</dc:creator>
  <dc:creator>ZandraFagernas</dc:creator>
  <dc:creator>Aida Andrades Valtueña</dc:creator>
  <dc:creator>Ido Bar</dc:creator>
  <dc:creator>Evan Floden</dc:creator>
  <dc:creator>alexandregilardet</dc:creator>
  <dc:creator>Maxime Garcia</dc:creator>
  <dc:creator>Patrick Hüther</dc:creator>
  <dc:creator>Phil Ewels</dc:creator>
  <dc:creator>Gisela Gabernet</dc:creator>
  <dc:creator>nf-core bot</dc:creator>
  <dc:creator>sc13-bioinf</dc:creator>
  <dc:creator>Charles Plessy</dc:creator>
  <dc:creator>Harshil Patel</dc:creator>
  <dc:creator>Olga Botvinnik</dc:creator>
  <dc:creator>Selina Carlhoff</dc:creator>
  <dc:creator>Alex Hübner</dc:creator>
  <dc:date>2021-03-16</dc:date>
  <dc:description>Added

#687 - Adds Kraken2 unique kmer counting report
#676 - Refactor help message / summary message formatting to automatic versions using nf-core library
#682 - Add AdapterRemoval --qualitymax flag to allow FASTQ Phred score range max more than 41

Fixed

#666 - Fixed input file staging for print_nuclear_contamination
#631 - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
#652 - Added note to documentation that when using --skip_collapse this will use paired-end alignment mode with mappers when using PE data
#626 - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty
Added note to documentation that when using --skip_collapse this will use paired-end alignment mode with mappers when using PE data
#673 - Fix Kraken database loading when loading from directory instead of compressed file
#688 - Allow pipeline to complete, even if Qualimap crashes due to an empty or corrupt BAM file for one sample/library
#683 - Sets --igenomes_ignore to true by default, as rarely used by users currently and makes resolving configs less complex
Added exit code 140 to re-tryable exit code list to account for certain scheduler wall-time limit fails
#672 - Removed java parameter from picard tools which could cause memory issues
#679 - Refactor within-process bash conditions to groovy/nextflow, due to incompatibility with some servers environments
#690 - Fixed ANGSD output mode for beagle by setting -doMajorMinor 1 as default in that case
#693 - Fixed broken TSV input validation for the Colour Chemistry column
#695 - Fixed incorrect -profile order in tutorials (originally written reversed due to nextflow bug)
#653 - Fixed file collision errors with sexdeterrmine for two same-named libraries with different strandedness

Dependencies

Bumped MultiQC to 1.10 for improved functionality
Bumped HOPS to 0.35 for MultiQC 1.10 compatibility
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  <dc:identifier>https://zenodo.org/record/4608332</dc:identifier>
  <dc:identifier>10.5281/zenodo.4608332</dc:identifier>
  <dc:identifier>oai:zenodo.org:4608332</dc:identifier>
  <dc:relation>url:https://github.com/nf-core/eager/tree/2.3.2</dc:relation>
  <dc:relation>doi:10.5281/zenodo.1465061</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:title>nf-core/eager: [2.3.2] - Aalen (Patch) - 2021-01-14</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
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