broadinstitute / viral-ngs / 1072

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remove rmdup from depletion call

remove rmdup from depletion call, remove *.rmdup.bam from positional arguments for depletion CLI parser, remove *.rmdup.bam from inputs where depletion is called (test cases, WDL), remove *.rmdup.bam from expected depletion outputs. Chance Snakemake merge_one_per_sample rule to call  rmdup_clumpify_bam rather than rmdup_mvicuna_bam

312 of 2751 branches covered (11.34%)

1458 of 6333 relevant lines covered (23.02%)

0.23 hits per line