Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

mkdocs-snakemake-rule-plugin error #124

Open
jonca79 opened this issue Jul 6, 2023 · 0 comments
Open

mkdocs-snakemake-rule-plugin error #124

jonca79 opened this issue Jul 6, 2023 · 0 comments
Assignees
Labels
bug Something isn't working

Comments

@jonca79
Copy link
Contributor

jonca79 commented Jul 6, 2023

The mkdocs-snakemake-rule-plugin can not handle the following input variable when creating the documentation:

rule glnexus:
input:
gvcfs=expand("snv_indels/deeptrio/{{sample}}_{{type}}/{trio_member}.g.vcf", trio_member=["child", "parent1", "parent2"]),

Error:
ERROR - Error reading page 'softwares.md': too many values to unpack (expected 2)
Traceback (most recent call last):
File "/home/jonas/Snakemake/venv/bin/mkdocs", line 8, in
sys.exit(cli())
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/click/core.py", line 1130, in call
return self.main(args, **kwargs)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(args, **kwargs)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs/main.py", line 234, in serve_command
serve.serve(dev_addr=dev_addr, livereload=livereload, watch=watch, **kwargs)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs/commands/serve.py", line 83, in serve
builder(config)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs/commands/serve.py", line 76, in builder
build(config, live_server=live_server, dirty=dirty)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs/commands/build.py", line 308, in build
_populate_page(file.page, config, files, dirty)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs/commands/build.py", line 177, in _populate_page
page.markdown = config.plugins.run_event(
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs/plugins.py", line 520, in run_event
result = method(item, **kwargs)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs_snakemake_rule_plugin/plugin.py", line 22, in on_page_markdown
return self.generator.get_markdown(markdown, **kwargs)
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs_snakemake_rule_plugin/markdown.py", line 279, in get_markdown
new_markdown = markdown_table(self.config_extracted_rules[rule_name]['source'],
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs_snakemake_rule_plugin/markdown.py", line 162, in markdown_table
variables = get_input_variabels(rule_source,
File "/home/jonas/Snakemake/venv/lib/python3.10/site-packages/mkdocs_snakemake_rule_plugin/markdown.py", line 99, in get_input_variabels
key, value = re.split("[ ]
=[ ]
", line)
ValueError: too many values to unpack (expected 2)

@jonca79 jonca79 added the bug Something isn't working label Jul 6, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants