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AlexanderLabWHOI / eukrhythmic

A metatranscriptomic pipeline optimized for the study of microeukaryotes.
MIT License
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metaT sample file naming #35

Closed cnatalie closed 4 years ago

cnatalie commented 4 years ago

metaT file does not handle "_" in sample file name. Example:

HN001_S1 works HN001 does not - results in float/string error

actual sample file name: HN001_S1_L002_R1_001.fastq.gz

akrinos commented 4 years ago

Do you mean that HN001 works, but HN001_S1 does not, @cnatalie?

cnatalie commented 4 years ago

Sorry! HN001 and HN001_S1 as both work as SampleNames with that raw file. Here is an example of one that does not:

C47M_47 - works C47M - does not:

TypeError in line 15 of /nas/longleaf/home/cnatalie/eukrhythmic/Snakefile:
must be str, not float

Sample file name: C47M_47_R1_001.fastq.gz

metaT file: SampleName SampleID AssemblyGroup FastqFile C47M C47M C47M C47M C32M C32M C32M C32M

akrinos commented 4 years ago

This was resolved in the following way: the fastqfile name should be different, in this case, because it doesn't include enough of the file name. In the future, this file should be simplified/not required for users to supply.