[2.4.5] - Wangen (Patch) - 2022-08-02

Added

Fixed

• #882 Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
• #879 Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
• #880 Fix failure of endorSpy to be cached or reexecuted on resume (♥ to @KathrinNaegele, @TCLamnidis, & @mahesh-panchal for reporting and debugging)
• #885 Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
• #887 Clarify what is considered 'ultra-short' reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
• #889 Remove/update parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
• #895 Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
• #897 Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting)
• #899 Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting)
• Fixed some missing default values in the nextflow parameter schema JSON
• #789 Substantial speed and memory optimisation of the extract_map_reads.py script (♥ to @ivelsko for reporting, @maxibor for optimisation)
• Fix staging of input bams for genotyping_pileupcaller process. Downstream changes from changes introduced when fixing endorspy caching.
• Made slight correction on metro map diagram regarding input data to SexDeterrmine (only BAM trimming output files)

Dependencies

• Updated MultiQC to latest stable alpha version on bioconda, correcting the previously nonsensical AdapterRemoval plots (♥ to @NiemannJ for fixing in MultiQC)

Deprecated