CODEWITHSUNDEEP
pythonshellsnakemake
Ester
Ester

Reputation: 21

Can't execute shell script in snakemake

I recently started using snakemake and would like to run a shell script in my snakefile. However, I'm having trouble accessing input, output and params. I would appreciate any advice!

Here the relevant code snippets:

  1. from my snakefile
rule ..:
    input:
        munged = 'results/munged.sumstats.gz'
    output:
        ldsc = 'results/ldsc.txt'
    params:
        mkdir = 'results/ldsc_results/',
        ldsc_sumstats = '/resources/ldsc_sumstats/',
    shell:
        'scripts/run_gc.sh'
  1. and the script:
chmod 770 {input.munged}
mkdir -p {params.mkdir}

ldsc=$(ls {params.ldsc_sumstats})
for i in $ldsc; do
...

I get the following error message:

...
chmod: cannot access '{input.munged}': No such file or directory
ls: cannot access '{params.ldsc_sumstats}': No such file or directory
...

Upvotes: 2

Views: 574

Answers (2)

Michael Hall
Michael Hall

Reputation: 3330

From v7.14.0 Snakemake now supports executing external Bash scripts, with access to snakemake objects inside. See the docs for example usage.

Upvotes: 1

SultanOrazbayev
SultanOrazbayev

Reputation: 16561

The syntax of using {} statements applies only to shell scripts defined within Snakefile, while in the example you provide, the script is defined externally.

If you want to use the script as an external script you will need to pass the relevant arguments (and parse them inside the shell script). Otherwise, it should be possible to copy-paste the script content inside the shell directive and let snakemake substitute the {} variables.

Upvotes: 2

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