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malariagen / pipelines

Pipelines for processing malaria parasite and mosquito genome sequence data.
MIT License
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Output of vector short read alignment pipeline is named *.bam.bam #68

Closed tnguyensanger closed 2 years ago

tnguyensanger commented 3 years ago

Fix so that it only has a single .bam suffix

tnguyensanger commented 3 years ago

Output of https://github.com/malariagen/pipelines/blob/master/pipelines/batch-import-short-read-alignment-and-genotyping-vector/farm5/BatchImportShortReadAlignmentAndGenotyping.wdl are inproperly named as .bam.bam.

See the outputs of the FixMateInformation task.