Sarek 3.0 - Skierfe

• Porting to DSL2
• Use CRAM files where possible
• Add new tools: DragMap, DeepVariant, Joint germline calling, Haplotypecaller single sample, CNVKit Somatic, Tiddit Somatic
• Replaced tools: Trimgalore -> Fastp, Qualimap -> Mosdepth
• New references: BWAMem2, DragMap, Germline Resource
• Add a new entry --step markduplicates
• Steps can be started from bam or cram files
• Added --paired_variant_calling_only to skip normal computations for paired samples
• Only unmatched tumor samples will be run in single mode
• Input fastq files are split by default and mapped in parallel
• Bam2Fastq: changed to using samtools
• Samplesheet is now in CSV format with a header line with improved validation and flexibility
• New parameter --skip_tools retires --skip_qc, --skip_markduplicates and --skip_bqsr
• --sequencing_center renamed to --seq_platform`
• New parameter --wes must be set for targeted data
• New parameter --save_bam_ouput to store results file in BAM format instead of CRAM
• Additional VEP output formats
• Additional VEP plugins: loftee, spliceAI, spliceRegions, dbnsfp
• Remove sentieon support

New Contributors

• @abhi18av made their first contribution in #394
• @nickhsmith made their first contribution in #454
• @emiller88 made their first contribution in #465
• @priesgo made their first contribution in #432
• @SusiJo made their first contribution in #545
• @asp8200 made their first contribution in #571
• @lassefolkersen made their first contribution in #591
• @WackerO made their first contribution in #570

Full Changelog: 2.7.2...3.0