According to samtools/markdup documentation, there are additional steps to be done before calling the markdup steps. This steps are performed by bam_markduplicates_samtoolsnf-core subworkflow, however they need to be performed before the sort step (that is done during alignment)
[x] install samtools/markdup module
[x] patch samtools/markdup module to produce reports
[ ] fix and rename cram_markduplicates_picard local subworflow
According to samtools/markdup documentation, there are additional steps to be done before calling the
markdupsteps. This steps are performed by bam_markduplicates_samtools nf-core subworkflow, however they need to be performed before thesortstep (that is done during alignment)samtools/markdupmodulesamtools/markdupmodule to produce reportsfix and renamecram_markduplicates_picardlocal subworflowbam_markduplicates_samtoolsnf-core workflowpicard/markduplicatesmodules and configurationsamtools/markdupwith MultiQC config--save_cramoption