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
Post-merge snakemake.params
#663
Conversation
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
The majority of the param conversion is done by a python algorithm. Some changes are simple, only changing the word "config" into "param". The complicated part is in I believe its better to just add in param |
Hey @virio-andreyana, I would not pass the whole config but use the sections which are really needed (even if it is a lot). Imagine you just want to alter some colours for the visualization of results (which happens after the solving), then the whole solving process would be retriggered. |
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
This is a re-do for the pull request in #296.
Changes proposed in this Pull Request
Use the
params:
section in rule definition to keep track of changed settings inconfig.yaml
.https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
The goal is that rules for which parameters have changed rerun automatically.
This can currently be done with:
https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-trigger-re-runs-for-rules-with-updated-code-or-parameters
snakemake -n -R `snakemake --list-params-changes`
or
snakemake -R $(snakemake --list-params-changes)
This will be even more convenient, once this
snakemake
PR is released:snakemake/snakemake#1107
or
(which would also include code changes)
It seems to work very nicely to pass lists/dicts as params, which would help us keep config "blocks".
This PR is not complete yet, but a proof-of-concept for a selection of config settings. We can discuss from here and complete later.
Rules Checklist
Script Checklist
Checklist
envs/environment.yaml
.config.default.yaml
.doc/configtables/*.csv
.doc/release_notes.rst
is added.