Incorporate quanTIseq into immune-deconv module

[sjspielman]

Purpose/implementation Section

What scientific question is your analysis addressing?

As discussed in issue #1238, this PR adds the quanTIseq method to the immune-deconv module.

What was your approach?

Slight modification of existing script to run deconvolution to export RDS files instead of .RData (for tracking different output names per method). We now call the deconvolution script twice from the analysis shell script, once per method. We also add a quick check into the R script to convert any provided method to all lowercase, which immunedeconv requires.

What GitHub issue does your pull request address?

1238

Results

What types of results are included (e.g., table, figure)?

Updated result files as RDS:

results/xcell_deconv-output.rds
results/quantiseq_deconv-output.rds

Reproducibility Checklist

• [x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• [x] This analysis has been added to continuous integration.

Documentation Checklist

• [x] This analysis module has a README and it is up to date.
• [x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• [x] The analytical code is documented and contains comments.