1.0.0

• Major overhaul to CyclomicsSeq, with a simpler workflow architecture. The EPI2ME interface and user guidelines on the README.md were also updated.
• Changed naming of important output files to contain the sample ID, a randomly generated unique run ID and the barcode (if present). Users can define the sample ID -- if undefined, a sample ID will be retrieved from a valid parent folder name.
• Added an argument enabling users to provide a BED file with genomic regions to be analysed (--region_file [regions.bed])
• Added support for input directories containing several barcode subdirectories with FASTQ files, where each subdirectory name is interpreted as a sample name. CyclomicsSeq will analyse each sample separately and output separate files and reports per sample.
• Added splitting of large FASTQ files per number of reads (--split_fastq_by_size [true] and --max_fastq_size [40000]).
• Added a filter for alignment rate to provided or detected regions of interest (--filter_by_alignment_rate [false] and --min_align_rate [0.8]).
• Updated docker container with seqkit version 2.9.0 and moved container to cyclomics/cyclomicsseq:0.8.2.
• Fixed an error in read structure donut plotting where reads with a single alignment were not being counted; adjusted function to be valid with coordinate-sorted BAM files.
• Fixed an issue where alignment was running out of memory due to inappropriate allocation.
• Fixed an issue where the annotated VCF output file was invalid due to a whitespace in COSMIC legacy ID tags.
• Minor plotting and report updates.
• Known contaminant detection has been temporarily disabled due to unknown Freebayes error.