Workflows #788
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Workflows #788
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This makes it much easier to understand the directory structure for each workflow.
Since we use these functions in workflows that are not in the anvio repository (like `export_locus.snake`), then I wish to keep them for now, and maybe forever.
of course, we can't do anything with them, but just listing them is also nice.
and also added flag references_mode to the config to be more verbose about it.
this option is there so we could check if a param was set by the user.
and should be a localrule
Now you can save a default config file for a workflow (but the only the contigs default config is actually accurate) You can list the available workflows In addition, contigs workflow now works and has been tested.
it's late, what do you want????
let's use this flag to let user define a config file path. one stone two birds.
- no more output file argument, because now the get-default-config requires a filename argument. - removing the entire if block to export default config into the base class. if the parameter set, it will save the default config for whicever workflow is set, and exit.
I commented out the dry-run steps because they actually start running things and I don't want that yet.
For now, it doesn't do anything yet, but at least the purpose is clear.
also, if the user set the value to a boolean False then don't return the default. This fixes that behavior
any other value will result in a negative result. maybe we should put a warning that the value should be either boolean true or false.
if user asked to save workflow graph we will also set `dry_run_only` to True
@meren, please tell me if this makes sense to you. The idea is that this would allow us to run: ``` anvi-run-snakemake-workflow -w contigs -c config.json --additional-params '--clustetr "-n {threads} -log {log}" --resources nodes=60'
This reverts commit 9a50aeb.
This is how I had to solve this. following an advice in the discussion here: https://bugs.python.org/issue9334
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@meren, I tested it on barhal to see that the |
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This is very happy news, Alon! Thank you very much. |
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:-) Thanks! |
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I think it is stable enough to be merged with master