need to add "--REMOVE_DUPLICATES" to MarkDuplicates

umb-oconnorgroup / plasmodium_snp_call_pipeline_wdl

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need to add "--REMOVE_DUPLICATES" to MarkDuplicates #2

Closed bguo068 closed 3 years ago

bguo068 commented 3 years ago

https://github.com/umb-oconnorgroup/plasmodium_snp_call_pipeline_wdl/blob/065c21cc4980fbbcc5f5b0c526014137090ab3fb/pipeline.wdl#L310-L312 misses the "--REMOVE_DUPLICATES" in the MarkDuplicates command

MarkDuplicates also produces a metrics file indicating the numbers of duplicates for both single- and paired-end reads

--REMOVE_DUPLICATES: If REMOVE_DUPLICATES is true, all duplicates are removed

bguo068 commented 3 years ago

fixed in commit 69908e609d6ceff21263c500e753511a7ef3ca79