millironx/nf-configs
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Change params.hostnames from map to string

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Harshil Patel 2021-11-02 10:37:53 +00:00
parent 0600ac1293
commit adeff52f89
2 changed files with 3 additions and 24 deletions
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6
README.md
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@ -66,12 +66,6 @@ See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for
Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values.
Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.
### Checking user hostnames
If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile.
Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name.
If the user's hostname contains this string at the start of a run or when a run fails and their profile does not contain the profile name, a warning message will be printed.
### Testing ### Testing
If you want to add a new custom config file to `nf-core/configs` please test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter. If you want to add a new custom config file to `nf-core/configs` please test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter.

21
nfcore_custom.config
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@ -61,23 +61,8 @@ profiles {
uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" } uzh { includeConfig "${params.custom_config_base}/conf/uzh.config" }
} }
// If user hostnames contain one of these substring and they are
// not running the associated profile, it will trigger a warning message
// Should be defined here for all profiles (not within profile config)
params { params {
// This is a groovy map, not a nextflow parameter set // Changed from a Groovy Map to a string for backwards compatibility
hostnames = [ // See https://github.com/nf-core/tools/issues/1304
binac: ['.binac.uni-tuebingen.de'], hostnames = ''
cbe: ['.cbe.vbc.ac.at'],
cfc: ['.hpc.uni-tuebingen.de'],
crick: ['.thecrick.org'],
genotoul: ['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'],
genouest: ['.genouest.org'],
icr_davros: ['.davros.compute.estate'],
imperial: ['.hpc.ic.ac.uk'],
imperial_mb: ['.hpc.ic.ac.uk'],
uppmax: ['.uppmax.uu.se'],
utd_ganymede: ['ganymede.utdallas.edu'],
utd_sysbio: ['sysbio.utdallas.edu']
]
} }