BUG When using fastq with no .gz suffixed, cell barcode can not be extracted.

[crotoc]

Thanks for fix my last bug and I encounter a new one.

Describe the bug A clear and concise description of what the bug is. In zUMIs.sh at line 257, pref=$(basename ${f} ) should be pref=$(basename ${f} .gz)

Because the former step is splitfq.sh, which will generate splitted gz files. If the .gz is not removed from basename of ${f}, it will result the line 96 of qfilter_v2.ql to add an extra .gz at the end of the splited gz files. Then no bam file can be produced and no cell barcode can be identified.

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[cziegenhain]

I would recommend to start with gzipped fastq files instead. We will probably retire the option for uncompressed input because it is not really practical.

[crotoc]

Okay. Thanks!