Software Open Access

nf-core/eager: [2.4.0] - 20201-09-14

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

Added
  • #317 Added bcftools stats for general genotyping statistics of VCF files
  • #651 - Adds removal of adapters specified in an AdapterRemoval adapter list file
  • #642 and #431 adds post-adapter removal barcode/fastq trimming
  • #769 - Adds lc_extrap mode to preseq (suggested by @roberta-davidson)
Fixed
  • Fixed some missing or incorrectly reported software versions
  • #771 Remove legacy code
  • Improved output documentation for MultiQC general stats table (thanks to @KathrinNaegele and @esalmela)
  • Improved output documentation for BowTie2 (thanks to @isinaltinkaya)
  • #612 Updated BAM trimming defaults to 0 to ensure no unwanted trimming when mixing half-UDG with no-UDG (thanks to @scarlhoff)
  • #722 Updated BWA mapping mapping parameters to latest recommendations - primarily alnn back to 0.01 and alno to 2 as per Oliva et al. 2021 (10.1093/bib/bbab076)
  • Updated workflow diagrams to reflect latest functionality
  • #787 Adds memory specification flags for the GATK UnifiedGenotyper and HaplotyperCaller steps (thanks to @nylander)
  • Fixed issue where MultiVCFAnalyzer would not pick up newly generated VCF files, when specifying additional VCF files.
  • #790 Fixed kraken2 report file-name collision when sample names have . in them
  • #792 Fixed java error messages for AdapterRemovalFixPrefix being hidden in output
  • #794 Aligned default test profile with nf-core standards (test_tsv is now test)
Dependencies
  • Bumped python: 3.7.3 -> 3.9.4
  • Bumped markdown: 3.2.2 -> 3.3.4
  • Bumped pymdown-extensions: 7.1 -> 8.2
  • Bumped pyments: 2.6.1 -> 2.9.0
  • Bumped adapterremoval: 2.3.1 -> 2.3.2
  • Bumped picard: 2.22.9 -> 2.26.0
  • Bumped samtools 1.9 -> 1.12
  • Bumped angsd: 0.933 -> 0.935
  • Bumped gatk4: 4.1.7.0 -> 4.2.0.0
  • Bumped multiqc: 1.10.1 -> 1.11
  • Bumped bedtools 2.29.2 -> 2.30.0
  • Bumped libiconv: 1.15 -> 1.16
  • Bumped preseq: 2.0.3 -> 3.1.2
  • Bumped bamutil: 1.0.14 -> 1.0.15
  • Bumped pysam: 0.15.4 -> 0.16.0
  • Bumped kraken2: 2.1.1 -> 2.1.2
  • Bumped pandas: 1.0.4 -> 1.2.4
  • Bumped freebayes: 1.3.2 -> 1.3.5
  • Bumped biopython: 1.76 -> 1.79
  • Bumped xopen: 0.9.0 -> 1.1.0
  • Bumped bowtie2: 2.4.2 -> 2.4.4
  • Bumped mapdamage2: 2.2.0 -> 2.2.1
  • Bumped bbmap: 38.87 -> 38.92
  • Added bcftools: 1.12
Deprecated
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