snakemake config file with path

Question

[QX]

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

[pbioinf]

Does your HPC use something like Lmod to manage dependencies?

[QX]

yes they could have share packages but I would like to use the packages in local folder, not via module load

[pbioinf]

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