Preparation of the config file about methylsnake HOT 6 CLOSED

If you are not using the provided wrapper script you will need to run Snakemake with --configfile because no default is provided inside the Snakefile.

In fact, my wrapper run_snakemake.sh should throw an error if not run as run_snakemake.sh path/to/config.yaml.

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So I can't make a dry run ?

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You can make a dry run but you need to add the path to the config file:

snakemake -n -p --configfile path/to/config.yaml

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Thanks! It worked :)
I have got this error message now.

WildcardError in line 221 of /exports/humgen/jihed/rrbs_zbtb24/MethylSnake/MethylSnake-1.1.1/Snakefile:
Wildcards in params cannot be determined from output files. Note that you have to use a function to deactivate automatic wildcard expansion in params strings, e.g., `lambda wildcards: '{test}'`. Also see https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules:
'diff'

Do I need to define a contrast in the config file?

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I pushed a fix, please, update your repositoty. Thanks for pointing out!

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Thanks the pipeline is now running. Note that I used the release 1.1.1 on a slurm computer.
I changed the Snakefile directly to make it work.

Thanks a lot! I hope to not have to bother you again! I learned a lot about Snakemake just by reading your pipeline!

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