Question: Unknown input filename in Snakemake
gravatar for Hansen_869
12 months ago by
Hansen_86920 wrote:


I have just assembled my bins from my contig files. For each contig file, is a corresponding folder, wherein the bins produced from the contig file reside. The amount of bins currently range from 20-80 depending on which contig file was used. Now, I want to look at the genes of the different bins. To do this, I must know the name of the input files to be used (I use Prokka). As my pipeline should be scaleable and the contig files used for binning will change during my research, I need a variable input. The bins are named like this (with "date" being the date the contig file was created): (date).001.fasta (date).002.fasta (date).003.fasta

And so forth. I have tried using asterisk like "(date).*.fasta", but without luck. Any suggestions?


snakemake • 277 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Hansen_86920
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