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Corrupted output if decontaminating more than one sample using Python API #25

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bede opened this issue Jul 23, 2023 · 1 comment
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Corrupted output if decontaminating more than one sample using Python API #25

bede opened this issue Jul 23, 2023 · 1 comment
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bede commented Jul 23, 2023

gen_clean_cmd() and gen_paired_clean_cmd() both mutate Aligner.cmd and Aligner.paired_cmd, and since Aligner is instantiated once, templating fails after processing the first fastq / pair of fastqs leading to corruption of the output of subsequent samples when using the Python API. Templating should not mutate Aligner instance. Needs tests for single and paired reads.
@bede bede added the bug Something isn't working label Jul 23, 2023
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bede commented Jul 23, 2023

Fixed in 50b9f53 / 0.1.0

@bede bede closed this as completed Jul 23, 2023
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