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Output of vector short read alignment pipeline is named *.bam.bam #68

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tnguyensanger opened this issue Dec 2, 2020 · 1 comment

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tnguyensanger commented Dec 2, 2020

Fix so that it only has a single .bam suffix

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tnguyensanger commented Dec 2, 2020

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.

tnguyensanger added a commit that referenced this issue


          Partially addresses #68, #54. Make sure output of FixMateInformation …

4f0f32d

…only has .bam suffix, not .bam.bam. Update README.md to reflect that run_ena is not required or used. Clean use of read_group_filename in WDL output

alimanfoo closed this as completed

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