Wildcards Snakemake using bedtools

Question

[Fadwa]

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

[Shred]

Please post your code for the Snakemake rule