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Add per-rule configuration capability #15

Merged
merged 23 commits into from
Apr 9, 2020
Merged

Add per-rule configuration capability #15

merged 23 commits into from
Apr 9, 2020

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mbhall88
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@mbhall88 mbhall88 commented Apr 8, 2020

This PR addresses the following:

Michael Hall added 18 commits April 7, 2020 15:25
create config class
4eea687
add concat params, get, and default params
ea56e44
add notebooks to ignore
24f51f4
add rule from params function to config
d658df0
add bool method for config
b4d301e
add default constructor to config
b02c1cd
add default queue to cookiecutter class
413489e 
add default queue to cookiecutter class
clean up submitter initialisation and allow passing config
6291d24
add missing test for cookiecutter default queue
43b4a94
add end-to-end test for rule-specific config
1565dfb
fix cookiecutter queue typo
3efab54
better naming of cluster log files [Snakemake-Profiles#14]
63bf7ff
fix typo in snakemake param in cookiecutter
2d16500 
typo
move directory logic into logdir so directories are created if not exist
6a54195 
[Snakemake-Profiles#14]
update default latency wait
3218443
update README
d064054
update pytest version requirements
d1e65be
Add contributing document
20af557
@mbhall88
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mbhall88 commented Apr 8, 2020

@leoisl could I please get a review when you get a chance?

leoisl
leoisl requested changes Apr 8, 2020
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Really nice PR, only minor comments from me.

Have you tested this profile in practice with the per-rule configuration?

{{cookiecutter.profile_name}}/lsf_config.py Outdated Show resolved Hide resolved
{{cookiecutter.profile_name}}/lsf_config.py Outdated Show resolved Hide resolved
{{cookiecutter.profile_name}}/lsf_submit.py Outdated Show resolved Hide resolved
{{cookiecutter.profile_name}}/lsf_submit.py Outdated Show resolved Hide resolved
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mbhall88 commented Apr 9, 2020

Have you tested this profile in practice with the per-rule configuration?

Yep.

leoisl
leoisl approved these changes Apr 9, 2020
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All fine for me!

@mbhall88 mbhall88 merged commit 137ca48 into Snakemake-Profiles:development Apr 9, 2020
@mbhall88 mbhall88 mentioned this pull request Apr 9, 2020
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@leoisl leoisl leoisl approved these changes

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