Adding a pipeline specific config for a specific system #85
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conf/pipeline/sarek/munin.config
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| params { | ||
| config_profile_contact = 'Maxime Garcia (@MaxUlysse)' | ||
| config_profile_description = 'sarek MUNIN profile provided by nf-core/configs.' |
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Presumably this overwrites the param set in the main config?
Line 3 in a283c5b
I guess this is fine.. Maybe not necessary though.
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Yes, the second config file overwrite all the params from the first one.
It would be better to append actually in that case.
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I do think it's good to keep that, that way you know that the main institute profile has been overwritten by a pipeline/institute config
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Not necessarily completely overwritten though. Most of the time it will be adding additional stuff I imagine.
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Existing params are overwritten
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But yeah, I do think it's good to know that this is more than the nf-core/configs classic institutional profile
pipeline/nfcore_custom_sarek.config
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| * ------------------------------------------------- | ||
| * nfcore custom profile Nextflow config file | ||
| * ------------------------------------------------- | ||
| * Config options for all custom environments. |
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It would be nice to update this a little to explain the difference to the main config profiles and mention that it's not necessary for all institutes / pipelines.
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I'm mainly playing now, but will make docs for that.
so that we can do that for UPPMAX as well
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Added some docs.
Please tell me what do you think about it.
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sorry for the commit mess in the end, I'll try rebasing |
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Both following commands worked as expected on munin. nextflow run MaxUlysse/sarek -r sentieon -profile test,munin --sentieon /
--custom_config_base 'https://raw.githubusercontent.com/MaxUlysse/nf-core_configs/sarek'nextflow run MaxUlysse/sarek -r sentieon -profile test,munin /
--custom_config_base 'https://raw.githubusercontent.com/MaxUlysse/nf-core_configs/sarek'All new params were used, and the sentieon specific module was only loaded (and container set to '' ) for all processes with the sentieon label when the params.sentieon was specified. |
rename file improve configs remove unnecessary params
Update conf/pipeline/sarek/munin.config
rename file improve configs remove unnecessary params
Update conf/pipeline/sarek/munin.config testing out module and containers collision
Update README.md Co-Authored-By: James A. Fellows Yates <[email protected]># This is a combination of 2 commits. Update README.md Update README.md Co-Authored-By: James A. Fellows Yates <[email protected]>
Co-Authored-By: Phil Ewels <[email protected]>
Co-Authored-By: Phil Ewels <[email protected]>
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Documentation is much improved @maxulysse ! Couple more clarifying edits.
Let me know if you want a beta-tester of the system - I have a test case to apply it on but would rather wait for a request to do so.
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If you're OK with my latest changes, then we can merge it, and I'll help you apply that to eager ;-) |
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Good with me (docs wise, code I'll leave to someone else ;)) |
cf: https://github.com/MaxUlysse/sarek/blob/38d113e2d5de4750849ece63ec33e380abd94e31/nextflow.config#L103-L108
from nf-core/sarek#66