A cookiecutter template for Snakemake workflows
License: MIT License
THIS HAS BEEN SUPERSEDED BY THE FOLLOWING TEMPLATE AND WILL NOT BE MAINTAINED FURTHER: https://github.com/snakemake-workflows/snakemake-workflow-template
Cookiecutter template for snakemake workflows.
Is cookiecutter-snakemake-workflow a Github template?
It says in the readme in Step 1
"Create a new github repository using this workflow as a template" : https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-repository-from-a-template
In that web page the instructions say to click on the "Use This Template" button but I don't see any. Do I have to request special access to it?
PB
When trying to instantiate the template using cookiecutter, I get the following exception:
Traceback (most recent call last):
File "/Users/Julian/Anaconda/bin/cookiecutter", line 6, in <module>
sys.exit(cookiecutter.cli.main())
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/cookiecutter/cli.py", line 123, in main
default_config=default_config,
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/cookiecutter/main.py", line 91, in cookiecutter
output_dir=output_dir
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/cookiecutter/generate.py", line 253, in generate_files
template_dir = find_template(repo_dir)
File "/Users/Julian/Anaconda/lib/python3.6/site-packages/cookiecutter/find.py", line 36, in find_template
raise NonTemplatedInputDirException
cookiecutter.exceptions.NonTemplatedInputDirException
This is using cookiecutter 1.5.1 on Python 3.6.
Isn't this exception occurring because of the structure of the template? Most examples I have seen have the actual template in a subdirectory (see https://github.com/drivendata/cookiecutter-data-science for example), which is named after the repo name or something similar.
The default template requires pandas to work, but that dependency is not accounted for in the template:
In workflow/rules/common.smk pandas is used:
import pandas as pdso the template doesn't work as shipped.
$ snakemake -j 1
ModuleNotFoundError in line 2 of rna-seq/workflow/rules/common.smk:
No module named 'pandas'
File "rna-seq/workflow/Snakefile", line 17, in <module>
File "rna-seq/workflow/rules/common.smk", line 2, in <module>
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