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peterk87 / nf-villumina

Generic viral Illumina sequence analysis pipeline
MIT License
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Filtered reads should be saved with .gz extension due to compression with pbgzip #15

Closed peterk87 closed 4 years ago

peterk87 commented 4 years ago

Taxonomically filtered reads should be saved with the .gz file extension since filter_classified_reads compresses the reads with pbgzip:

cmd = f'seqtk subseq {reads_path} - | pbgzip -c > {output_path}'

https://github.com/peterk87/filter_classified_reads/blob/9ed907d471e5de5e51c1b3ba2ec5fe50870558a4/filter_classified_reads/io.py#L59