Reorder output folder structure

[daisymut]

• now .bam are in ${outdir}/bwa and .bam.bai are in ${outdir}/samtools

Tasks

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1. genome/ containing bwa index (if created in the run with --save-reference) and genome.sizes
2. (optional) alignment/bwa/ containing bam and associated bai files
3. alignment/markduplicates/ containing dup marked bam and associated bai files
4. single_tracks/deeptiools/ containing bigwig .bw files
5. (optional) comparisons/spp_mle/ containing pairwise bigwig .bw files