Missing Pre-alignments with RefGenie in v0.10.0

[CriticalSci]

Hi @jpsmith5,

I recently installed PEPPRO on our cluster following the conda installation instructions. Everything appears to run fine except for the pre-alignment step. No matter what I define in the looper yaml input file, the pre-alignment to human_rDNA never happens and gets skipped despite having all the necessary RefGenie assets.

PEPPRO_log.md:

### Arguments passed to pipeline:
* `prealignment_index`:  `[]`
* `prealignment_names`:  `[]`
### Prealignments (04-13 18:55:48) elapsed: 251.0 _TIME_

You may use `--prealignment-index` to align to references before the genome alignment step. See http://peppro.databio.org/en/latest/ for documentation.

refgenie list lists:

genome	assets
hg38	fasta, bowtie2_index, ensembl_gtf, ensembl_rb, refgene_anno, feat_annotation
human_rDNA	fasta, bowtie2_index

I defined the prealignments in the yaml as per the examples in the repo:

  imply:
    - if:
        organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"]
      then:
        genome: "hg38"
        prealignments: ["human_rDNA"] # also tried "human_rDNA"

The same input data/yaml/csv runs fine on the 0.9.11 PEPPRO install on a local machine though. I noticed there's been a lot of changes regarding RefGenie / prealignment code in peppro.py since 0.9.11 so perhaps you have a better idea of what could be going wrong with 0.10.0? Cheers!