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