Note: I've tweaked some of the DSL1 linting YML/files to make them work again so they've been added to the ignore stuff of the nf-core.yml.
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/updated 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.
Dependencies
Updated MultiQC to latest stable alpha version on bioconda, correcting the previously nonsensical AdapterRemoval plots (♥ to @NiemannJ for fixing in MultiQC)
[2.4.5] - 2022-07-39
Note: I've tweaked some of the DSL1 linting YML/files to make them work again so they've been added to the ignore stuff of the nf-core.yml.
Added
Fixed
extract_map_reads.py
script (♥ to @ivelsko for reporting, @maxibor for optimisation)Dependencies
Deprecated