Sample table format/config file specification

[taylorreiter]

Hi @SilasK! I see that the snakefile reads in a sample table referenced in the config file (https://github.com/SilasK/amplicon-seq-dada2/blob/master/Snakefile#L5):

SampleTable = pd.read_table(config['sampletable'],index_col=0)

but I can't find an example of a sample table, and I don't see the sample table referenced in the config file. Would you be willing to provide an example?

[SilasK]

Sorry, I was on holidays. I try to answer your questions asap.

[SilasK]

@taylorreiter I added some more infos, a conda env and a test script. This should help you to use the pipeline.

Somethimes there are RSV that are much shorter than the expected length. Therefore I added a step where I filter the amplicon for length variation. I don't know if this interferes with an ITS. But you can set a very high number in the config file.

[taylorreiter]

Thank you!!