Overriding yaml file paths using parameters in dockerless mode

[gongyixiao]

neoantigen-vaccine-pipeline/run_snakemake.py

Lines 335 to 339 in d2af22c

	# replace /outputs, /reference-genome, /inputs paths in config with user-specified dirs
	configfile_contents = configfile_contents.replace(
	'/outputs', args.outputs).replace(
	'/reference-genome', args.reference_genome).replace(
	'/inputs', args.inputs)

This is not practical to do.

Basically if you want to override the the tumor fastq files in the input for example using the below file:
/home/user/tumor/tumor.fastq.gz

What you need to put into the yaml file is
/home/user/inputs/tumor.fastq.gz
and use the below argument:
--inputs /tumor/

I don't think it makes any sense since these are all non existing paths

Same thing for --outputs and --reference-genome

Even worse, if you have multiple /inputs words in your path, they will all be replaced by --inputs and it will never be correct. /home/user/inputs/fastq/tumor/tumor.fastq.gz has to be /home/user/inputs/fastq/inputs/tumor.fastq.gz and will be replaced by --inputs /tumor and become /home/user/tumor/fastq/tumor/tumor/fastq.gz.

Due to the way the program wrote to parse the parameters, I think it's not an easy fix. But I think it's really necessary to make the change for Dockerless run or singularity run working.