snakemake and snakefile question.

Question

[Andy]

Hello,

I am trying to install the scIB pipeline based on the instruction on GitHub. However, I encountered a problem about snakefile and snakmake.

The command line give by instruction is:

snakemake metrics --configfile configs/test_data-R${{ matrix.R }}_small.yaml -kc1

The author provide snakefile for each steps. I am not sure how to processed.

This is my first time know snakefile and snakemake. I was guessing I should excuse snakefile first? or snakemake command will execute snakefile? However, the error is no command for snakemake.

Could you please offer some hits for me? Thanks!

Andy

[Andy]

I think I understand a little bit, snakemake command will run snakefile in the current directory, and we need to mv snakefile.txt to snakefile.

[Jesse]

That's right, it defaults to looking for either Snakefile or snakefile in the current directory. (You could use a different name if you wanted to with something like snakemake --snakefile snakefile.txt metrics ....)