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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

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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nf-core/eager-2.3.2.zip
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