Snakemake: HISAT2 alignment of many RNAseq reads against many genomes

I have several genome files, all with suffix .1.ht2l to .8.ht2l bob.1.ht2l bob.2.ht2l bob.3.ht2l bob.4.ht2l bob.5.ht2l bob.6.ht2l bob.7.ht2l bob.8.ht2l steve.1.ht2l ….steve.8.ht2l and so on and sereval RNAseq samples, like flower_kevin_1.fastq.gz flower_kevin_2.fastq.gz flower_daniel_1.fastq.gz flower_daniel_2.fastq.gz and so on also with different tissues. I would like to align all rnaseq reds against the genomes. UPDATED: workdir: “/path/to/aligned” (HISAT2_INDEX_PREFIX,)=glob_wildcards(“/path/to/index/{prefix}.1.ht2l”)…

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