⚡ replace picard/markduplicates with samtools/markdup

[bunop]

According to samtools/markdup documentation, there are additional steps to be done before calling the markdup steps. This steps are performed by bam_markduplicates_samtools nf-core subworkflow, however they need to be performed before the sort step (that is done during alignment)

• install samtools/markdup module
• patch samtools/markdup module to produce reports
• fix and rename cram_markduplicates_picard local subworflow
• install bam_markduplicates_samtools nf-core workflow
• remove picard/markduplicates modules and configuration
• check samtools/markdup with MultiQC config
• test --save_cram option