Seqera containers: POC 3 #45
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Tried to set the base registry, not 100% how it works with the |
| def mod_container = switch([workflow.containerEngine, workflow.profile]) { | ||
| case {it[0] == 'singularity' && it[1].contains('arm')} -> 'click_pandas_plotly_express_typing:3fe674b9fa7b15b8' | ||
| case {it[0] == 'singularity'} -> 'click_pandas_plotly_express_typing:a4af841350996386' | ||
| case {it[1].contains('arm')} -> 'click_pandas_plotly_express_typing:2e5e17c7ed2d1115' | ||
| default -> 'click_pandas_plotly_express_typing:21adb9e2d1b605a5' | ||
| } |
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These mod_container definitions should be wrapped into functions, as currently the formal grammar does not support global variable definitions
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Also switch expressions are not currently supported, as I would like to leave room for us to eventually provide our own pattern matching syntax
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that's yet another horrible boilerplate code. -1
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@ewels can this be moved to a config file in the module directory? it would be easier to generate that way. and the pipeline config should include it under a profile
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Interesting idea - so a module config, but that is simply imported by the pipeline config. I like it! I'll whip up a POC No.4.
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I think one goal of the new config parser is to remove custom code from the config
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I think I should be able to do it with profiles - the same as POC No.1, but just split up into config files that are bundled with the module 🤔
Dinner now but I'll try later / tomorrow.
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@bentsherman - done in #46
Seqera Containers: Proof of concept No. 3
Hardcode container URIs at module level.
Workflow for generating:
nextflow.configWorkflow for usage: (Identical to current usage)
nextflow run -profile dockerorsingularity,armetc. (profile names up for refinement). Same as current.nf-core downloadas done currently, no change needed.