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.
https://github.com/openvax/neoantigen-vaccine-pipeline/blob/d2af22c68a93a4b7b5e36d740fb16bdd84f5feb8/run_snakemake.py#L335-L339
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.gzWhat you need to put into the
yamlfile is/home/user/inputs/tumor.fastq.gzand use the below argument:--inputs /tumor/I don't think it makes any sense since these are all non existing paths
Same thing for
--outputsand--reference-genomeEven worse, if you have multiple
/inputswords in your path, they will all be replaced by--inputsand it will never be correct./home/user/inputs/fastq/tumor/tumor.fastq.gzhas to be/home/user/inputs/fastq/inputs/tumor.fastq.gzand will be replaced by--inputs /tumorand 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.