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Describe the bug
When I try to lint my workflow, which contains a remote module import (from github), the lint fails even though I can run the workflow. As far as I can tell from the release notes, the bug has not been fixed yet.
Logs
My code:
module wgs_std_viper:
snakefile: "https://github.com/marrip/wgs_std_viper/raw/develop/Snakefile"
config: config
use rule * from wgs_std_viper as wgs_std_*
And the output of the linter:
Traceback (most recent call last):
File "/home/vagrant/.conda/envs/snakemake/lib/python3.9/site-packages/snakemake/__init__.py", line 598, in snakemake
success = not workflow.lint(json=lint == "json")
File "/home/vagrant/.conda/envs/snakemake/lib/python3.9/site-packages/snakemake/workflow.py", line 282, in lint
json_snakefile_lints, snakefile_linted = SnakefileLinter(
File "/home/vagrant/.conda/envs/snakemake/lib/python3.9/site-packages/snakemake/linting/__init__.py", line 23, in lint
item_lints = [
File "/home/vagrant/.conda/envs/snakemake/lib/python3.9/site-packages/snakemake/linting/__init__.py", line 26, in <listcomp>
for lint in lint_item(self.read_item(item))
File "/home/vagrant/.conda/envs/snakemake/lib/python3.9/site-packages/snakemake/linting/snakefiles.py", line 18, in read_item
return open(snakefile).read()
FileNotFoundError: [Errno 2] No such file or directory: 'https://github.com/marrip/wgs_std_viper/raw/develop/Snakefile'
The text was updated successfully, but these errors were encountered:
Version
6.5.3
Describe the bug
When I try to lint my workflow, which contains a remote module import (from github), the lint fails even though I can run the workflow. As far as I can tell from the release notes, the bug has not been fixed yet.
Logs
My code:
And the output of the linter:
The text was updated successfully, but these errors were encountered: