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stjudecloud / workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.
MIT License
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Picard sort task fails for non-coordinate sorts #155

Closed adthrasher closed 3 months ago

adthrasher commented 3 months ago

In our implementation of the Picard sort, we attempt to move the bam index file since Picard uses the wrong name. However, the index file is only created if the sort order is coordinate. For other settings, this step will fail.

https://github.com/stjudecloud/workflows/blob/99827132a8d2e6e84bcfe38403dfe821efaffaca/tools/picard.wdl#L321