Simplify authentication output folders, filenames

[clami66]

Here I have removed one level of directory (from taxid/refid to taxid/). In order to keep track of what reference is used, I renamed the bam/sam/fasta files with the refid instead. I have also simplified the maltextract output dirname.

Here is how the outputs looked before:

tree .test/results/AUTHENTICATION/bar/632/
.test/results/AUTHENTICATION/bar/632/
├── bar.trimmed.rma6_MaltExtract_output
...
├── node_list.txt
└── ref_64
    ├── 632.bam
    ├── 632.breadth_of_coverage
    ├── 632.fasta
    ├── 632.PMDscores.txt
    ├── 632.read_length.txt
    ├── 632.sam
    ├── 632.sorted.bam
    ├── 632.sorted.bam.bai
    ├── authentication_scores.txt
    ├── authentic_Sample_bar.trimmed.rma6_TaxID_632.pdf
    ├── name.list
    ├── plotPMD.Rout
    ├── PMD_plot.frag.pdf
    └── PMD_temp.txt

27 directories, 52 files

how they looks now:

 tree .test/results/AUTHENTICATION/bar/632/
.test/results/AUTHENTICATION/bar/632/
├── authentication_scores.txt
├── authentic_Sample_bar.trimmed.rma6_TaxID_632.pdf
├── breadth_of_coverage
├── MaltExtract_output
...
├── name_list.txt
├── node_list.txt
├── plotPMD.Rout
├── PMD_plot.frag.pdf
├── PMDscores.txt
├── PMD_temp.txt
├── read_length.txt
├── ref_64.bam
├── ref_64.fasta
├── ref_64.sam
├── sorted.bam
└── sorted.bam.bai

26 directories, 52 files