Wildcards Snakemake using bedtools
Hi everyone, I need your help resolving this problem.
I'm working on diploide chromosome, and each chromosome has 2 haplotypes.
To run my snakemake, I started with two repertoire containing:
- Haplotype:
- chr_1.gff
- chr_2.gff
- NLR-annotator:
- chr_1.gff
- chr_2.gff
I need to run Bedtools to intersect Chr_1.gff in Haplotype with Chr_1.gff in NLR-annotator.
The problem is that generate two output, chr_1 [haplotype] vs chr_1[NLR-Annotator] and chr1_[haplotype] vs chr_2 [NLR-Annotatr]. I need only the intersection when the filenames match together.
I used wildcards but it doesn't work.
Thank you in advance
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