Use more wildcards

[marcelm]

This PR is in preparation for parallelization by chromosome. It is mainly about replacing the hard-coded BAM and VCF paths with wildcards.

For example, instead of creating mapped.sorted.tag.bam from mapped.sorted.bam, the rule was modified to create {base}.sorted.tag.bam from {base}.sorted.bam. Since we’ll have multiple BAM files when we split and parallelize by chromosome, this is necessary because we want the rule to apply to the BAMs for each chromosome.

Since this single change is quite invasive, I wanted to give you the chance to look at it in a separate, smaller PR (I can split this up even further if you want).

Another change is that there’s now a file named mapping.calling.bam, which is the fully preprocessed BAM file. The name of this file no longer depends on whether BQSR was done or not, so all the rules that need that file no longer have to use a variable to refer to it.

[pontushojer]

I think it all look good, some minor comments only. I am fine with keeping this as one PR.

[marcelm]

I’ve backed out the log file name changes for now. Should be ready for merging now.