Running external scripts with wildcards in snakemake - snakemake

Question

I am trying to run a snakemake rule with an external script that contains a wildcard as noted in the snakemake reathedocs. However I am running into KeyError when running snakemake.
For example, if we have the following rule:
SAMPLE = ['test']
rule all:
input:
expand("output/{sample}.txt", sample=SAMPLE)
rule NAME:
input: "workflow/scripts/{sample}.R"
output: "output/{sample}.txt",
script: "workflow/scripts/{wildcards.sample}.R"
with the script workflow/scripts/test.R containing the following code
out.path = snakemake#output[[1]]
out = "Hello World"
writeLines(out, out.path)
I get the following error when trying to execute snakemake.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 NAME
1 all
2
[Fri May 21 12:04:55 2021]
rule NAME:
input: workflow/scripts/test.R
output: output/test.txt
jobid: 1
wildcards: sample=test
[Fri May 21 12:04:55 2021]
Error in rule NAME:
jobid: 1
output: output/test.txt
RuleException:
KeyError in line 14 of /sc/arion/projects/LOAD/Projects/sandbox/Snakefile:
'wildcards'
File "/sc/arion/work/andres12/conda/envs/py38/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2231, in run_wrapper
File "/sc/arion/projects/LOAD/Projects/sandbox/Snakefile", line 14, in __rule_NAME
File "/sc/arion/work/andres12/conda/envs/py38/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 560, in _callback
File "/sc/arion/work/andres12/conda/envs/py38/lib/python3.8/concurrent/futures/thread.py", line 57, in run
File "/sc/arion/work/andres12/conda/envs/py38/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 546, in cached_or_run
File "/sc/arion/work/andres12/conda/envs/py38/lib/python3.8/site-packages/snakemake/executors/__init__.py", line 2262, in run_wrapper
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /sc/arion/projects/LOAD/Projects/sandbox/.snakemake/log/2021-05-21T120454.713963.snakemake.log
Does anyone know why this not working correctly?

Answer 1

I agree with Dmitry Kuzminov that having a script depending on a wildcard is odd. Maybe there are better solutions.
Anyway, this below works for me on snakemake 6.0.0. Note that in your R script snakemake#output[1] should be snakemake#output[[1]], but that doesn't give the problem you report.
SAMPLE = ['test']
rule all:
input:
expand("output/{sample}.txt", sample=SAMPLE)
rule make_script:
output:
"workflow/scripts/{sample}.R",
shell:
r"""
echo 'out.path = snakemake#output[[1]]' > {output}
echo 'out = "Hello World"' >> {output}
echo 'writeLines(out, out.path)' >> {output}
"""
rule NAME:
input:
"workflow/scripts/{sample}.R"
output:
"output/{sample}.txt",
script:
"workflow/scripts/{wildcards.sample}.R"