I'm not sure this is the right place for this question, but please let me know if it's not.
I'm currently using Snakemake to annotate some genes. I have a config file, in which my fastq filenames are listed. It looks something like this:
Samples: Sample A: R1: SampleA_R1.fq.gz R2: SampleA_R2.fq.gz Sample B: R1: SampleB_R1.fq.gz R2: SampleB_R2.fq.gz
This is just a simplification of the config file, as it is much longer, but the pattern is the same. Now, I want to concatenate SampleA R1 and SampleA R2 into one fq.gz file. The same goes for Sample B and so forth, if the config was longer. I guess I should be using wildcards, but I'm unsure about how to access the config file and how to use it with wildcards.
Thanks in advance!!