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 ${f}, it will result the line 96 of qfilter_v2.ql to add an extra .gz at the end of the splited gz files. Then no bam file can be produced and no cell barcode can be identified.
To Reproduce
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Desktop (please complete the following information):
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Version [e.g. 22]
Additional context
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I would recommend to start with gzipped fastq files instead. We will probably retire the option for uncompressed input because it is not really practical.
Thanks for fix my last bug and I encounter a new one.
Describe the bug A clear and concise description of what the bug is. In zUMIs.sh at line 257, pref=$(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.
To Reproduce Provide the YAML file and full standard output.
Screenshots If applicable, add screenshots to help explain your problem.
Desktop (please complete the following information):
Additional context Add any other context about the problem here.