snakemake config file with path
Hi all,
I am learning the snakemake for my pipeline.
For snakefile I am specifying my configfile: configfile: "./config.yaml"
In the config.yaml, I have software:
bwa: /hpc/lab/bin/bwa-0.7.17/bwa for calling bwa software from a path.
However, the /hpc/lab/bin/ happens to appear alots for all softs I used.
Is there a way to assign the path to variable, let say soft: /hpc/lab/bin/ and call it for bwa: ${soft}/bwa-0.7.17/bwa in yaml like in bash scrip?
Thank
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Does your HPC use something like Lmod to manage dependencies?
yes they could have share packages but I would like to use the packages in local folder, not via module load
In that case the best option would probably be to use snakemake's built-in conda environment manager to manage dependencies.
https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management