[2.4.3] - Wangen (Patch) - 2022-03-24

[2.4.3] - 2022-03-24

Added

Fixed

• #828 Improved error message if required metagenomic screening parameters not set correctly
• #836 Remove deprecated parameters from test profiles
• #838 Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
• #843 Re-add direct piping of AdapterRemovalFixPrefix to pigz
• #844 Fixed reference masking prior to pmdtools
• #845 Updates parameter documention to specify -s preseq parameter also applies to lc_extrap
• #851 Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample (♥ to @alexandregilardet for reporting)
• Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
• #857 Corrected samtools fastq flag to retain read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
• #866 Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)
• Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting and correcting)

Dependencies

• #829 Bumped sequencetools: 1.4.0.5 -> 1.5.2
• Bumped MultiQC: 1.11 -> 1.12 (for run-time optimisation and tool citation information)

Deprecated