Level3 modules new directory for prepare step

[gillissierra]

The prepared mafs from the generate_smg_inputs.R lcr-script are now in their own directory. Input file symlinks are named using wildcards to better track which files were used as inputs. Level3 modules that were tested with this new setup and the prepare step using threads, as in this PR:

• gistic2
• dnds
• mutsig
• rainstorm
• fishhook
• hotmaps
• oncodrivefml
• oncodriveclustl

Pull Request Checklists

If applicable

• [x] I added more granular output subdirectories.

Checklist for Updated Module

Important! If you are updating the module version, ensure the previous version of the module is restored from master. If you want to restore a deleted file or directory from the remote master, you can use git checkout origin/master path/to/file, then a git commit will ensure that file is tracked on your branch again. Example:

mv modules/strelka/1.1 modules/strelka/1.2
git checkout origin/master modules/strelka/1.1

Once moved to the new directory, change the version number in the op.setup_module section of the snakefile, .e.g

CFG = op.setup_module(
    name = "strelka",
    version = "1.2",
    subdirectories = ["inputs", "chrom_bed", "strelka", "filtered", "outputs"]
)

[gillissierra]

version bumps complete