nf-core/sarek — FASTQ-to-VCF Variant Calling

Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR against the GATK GRCh38 resource bundle (dbSNP, Mills/1000G indels), and selects callers — explicitly correcting that sarek defaults to Strelka when --tools is unset (pass haplotypecaller for GATK best practice or deepvariant for CNN accuracy), with a non-Nextflow manual GATK4 fallback. Use when the user wants a variant-calling pipeline, FASTQ to VCF, germline or somatic SNV/indel calling, nf-core/sare…