POC of new meta.yml structure and ontologies #5867
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mirpedrol
requested review from
drpatelh,
maxulysse,
abhi18av,
bunop,
jfy133,
ewels,
KevinMenden and
merszym
as code owners
| homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" | ||
| documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" | ||
| tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" | ||
| doi: "10.1101/105346" | ||
| licence: "['GPL v3']" | ||
| licence: ["GPL v3"] | ||
| identifier: biotools:atlas_db |
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Should just be atlas, not atlas_db in this case: https://bio.tools/atlas
| qualifier: val | ||
| type: map |
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@bentsherman - does this look about right to you, in terms of what we call things here?
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what's the use of adding the qualifier when you already have the type?
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The qualifier can be useful to know if two modules have the same inputs and outputs.
For example, we could have the case where two different outputs have type string, but the qualifier is val and env.
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You mean to check if the modules can be chained? In that case it doesn't matter if it a val or env, as long as they are both strings
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I am more thinking of a setting where modules can be interchangeable, for example for benchmarking of different tools. I would like to make sure that using aligner1 and using aligner2, both inputs and outputs will be exactly the same.
I know this can already be done with if/else and operating the channels if needed. But in the future, it would be cool if we can use this to automatically add any module which matches the requirements.
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Even there it doesn't matter if the string input is a val or env, as long as it is a string they are interchangeable.
The only difference is that val says "provide this value as a variable" whereas env says "provide this value as an environment variable", but those details are internal to the process
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OK, I see what you mean! Would it be best to remove the qualifier?
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Yeah, now you have merge conflicts 😓 Sorry @mirpedrol ! |
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I have updated the branch and solved conflicts for all modules here #6015 |
POC for nf-core/tools#3028 and nf-core/tools#3032
Run
nf-core modules lint <module_name> --fixfor modules:fastpsamtools/sortsamtools/indexatlas/splitmergepearmultiqcbwa/memNote that linting won't pass until #5837 is merged
ℹ️ The bio.tools ID was not automatically found for
bwa.ℹ️ The modules
samtools/index,atlas/splitmergeandbwa/memhad wrong channels specified or missing inputs/outputs, thus the resulting modifiedmeta.ymlhad to be fixed manually.Ontology for input and output files were added for
bwa/memas an example.