I'm using regex in snakemake wildcards but I've come accross an error that I don't understand.
In this shortened example it works:
rule graphviz:
input: "{graph}.dot"
output: "{graph}.{ext,(pdf|png)}"
shell: "dot -T{wildcards.ext} -o {output} {input}"
In this example, it doesn't:
## This is working
rule fastqc:
input: "{reads}.fastq"
output: "{reads}_fastqc/{sample}_fastqc.html"
shell:"fastqc --format fastq {input}"
## This is not working
rule fastqc:
input: "{reads}.{ext,(bam|fastq)}"
output: "{reads}_fastqc/{sample}_fastqc.html"
shell:"fastqc --format {wildcards.ext} {input}"
I'm attaching a screencap of the error message I'm getting. Thanks for your help.