nf-core/sarek: 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 https://github.com/nf-core/sarek/pull/394 @nickhsmith made their first contribution in https://github.com/nf-core/sarek/pull/454 @Emiller88 made their first contribution in https://github.com/nf-core/sarek/pull/465 @priesgo made their first contribution in https://github.com/nf-core/sarek/pull/432 @SusiJo made their first contribution in https://github.com/nf-core/sarek/pull/545 @asp8200 made their first contribution in https://github.com/nf-core/sarek/pull/571 @lassefolkersen made their first contribution in https://github.com/nf-core/sarek/pull/591 @WackerO made their first contribution in https://github.com/nf-core/sarek/pull/570 Full Changelog: https://github.com/nf-core/sarek/compare/2.7.2...3.