bwa-mem2 dependancy not found

[dmontemayor]

Describe the bug snakemake cannot build the bwa2_index rule from the bwa.yaml file

To Reproduce Steps to reproduce the behavior:

1. build and activate RSeq conda environment as specified in README
2. Run bash RSeq -e SRX1025899 -m DRIP

Expected behavior Should find bwa-mem2 and build the rule

Screenshots

Parsing input...

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.3     ✔ purrr   0.3.4
✔ tibble  3.1.1     ✔ dplyr   1.0.5
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   1.4.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Building DAG of jobs...
Building DAG of jobs...
Creating conda environment helpers/envs/bwa.yaml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /Users/daniel/Documents/GitHub/RSeq/helpers/envs/bwa.yaml:
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

ResolvePackageNotFound: 
  - bwa-mem2

  File "/Users/daniel/miniconda3/envs/RSeq/lib/python3.9/site-packages/snakemake/deployment/conda.py", line 388, in create

Additional context issues with macOS mentioned here and here

[millerh1]

Fixed