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Merge pull request #33 from ewels/master

Removed params.config_profile_name, added params.hostnames
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Harshil Patel 2019-03-13 16:49:43 +00:00 committed by GitHub
commit 8bc975c8c3
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16 changed files with 28 additions and 30 deletions

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@ -58,7 +58,14 @@ nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_co
If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
Please also make sure to add an extra `params` section with `params. config_profile_name`, `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. 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.
## 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

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'BINAC'
config_profile_description = 'BINAC cluster profile provided by nf-core/configs.' config_profile_description = 'BINAC cluster profile provided by nf-core/configs.'
config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC' config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'CCGA'
config_profile_description = 'CCGA cluster profile provided by nf-core/configs.' config_profile_description = 'CCGA cluster profile provided by nf-core/configs.'
config_profile_contact = 'Marc Hoeppner (@marchoeppner)' config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
config_profile_url = 'https://www.ikmb.uni-kiel.de/' config_profile_url = 'https://www.ikmb.uni-kiel.de/'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'CFC'
config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.' config_profile_description = 'QBiC Core Facility cluster profile provided by nf-core/configs.'
config_profile_contact = 'Alexander Peltzer (@apeltzer)' config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'http://qbic.uni-tuebingen.de/' config_profile_url = 'http://qbic.uni-tuebingen.de/'

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@ -1,8 +1,7 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'CRICK'
config_profile_description = 'The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.' config_profile_description = 'The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.'
config_profile_contact = 'Harshil Patel (@drpatelh )' config_profile_contact = 'Harshil Patel (@drpatelh)'
config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies' config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies'
} }

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@ -1,11 +1,9 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------- params {
* Nextflow config file for GIS (Aquila) config_profile_description = 'Genome Institute of Singapore (Aquila) cluster profile provided by nf-core/configs.'
* ------------------------------------------------- config_profile_contact = 'Andreas Wilm (@andreas-wilm)'
* Defines reference genomes, using iGenome paths config_profile_url = 'https://www.a-star.edu.sg/gis/'
* Imported under the default 'standard' Nextflow }
* profile in nextflow.config
*/
process { process {
executor = 'sge' executor = 'sge'
@ -20,4 +18,3 @@ params {
// illumina iGenomes reference file paths on GIS Aquila // illumina iGenomes reference file paths on GIS Aquila
igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/' igenomes_base = '/mnt/projects/rpd/genomes.testing/S3_igenomes/'
} }

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@ -1,8 +1,7 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'HEBBE'
config_profile_description = 'Gothenburg Hebbe cluster profile provided by nf-core/configs.' config_profile_description = 'Gothenburg Hebbe cluster profile provided by nf-core/configs.'
config_profile_contact = 'Phil Ewels (@ewels )' config_profile_contact = 'Phil Ewels (@ewels)'
config_profile_url = 'http://www.c3se.chalmers.se/index.php/Hebbe' config_profile_url = 'http://www.c3se.chalmers.se/index.php/Hebbe'
} }

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'MENDEL'
config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs' config_profile_description = 'GMI MENDEL cluster profile provided by nf-core/configs'
config_profile_contact = 'Patrick Hüther (@phue)' config_profile_contact = 'Patrick Hüther (@phue)'
config_profile_url = 'http://www.gmi.oeaw.ac.at/' config_profile_url = 'http://www.gmi.oeaw.ac.at/'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'MUNIN'
config_profile_description = 'Big iron cluster profile provided by nf-core/configs.' config_profile_description = 'Big iron cluster profile provided by nf-core/configs.'
config_profile_contact = 'Szilveszter Juhos (@szilva)' config_profile_contact = 'Szilveszter Juhos (@szilva)'
config_profile_url = '' config_profile_url = ''

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'PHOENIX'
config_profile_description = 'University of Adelaide Phoenix HPC cluster profile provided by nf-core/configs' config_profile_description = 'University of Adelaide Phoenix HPC cluster profile provided by nf-core/configs'
config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)' config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)'
config_profile_url = 'https://www.adelaide.edu.au/phoenix/' config_profile_url = 'https://www.adelaide.edu.au/phoenix/'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'SHH'
config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.' config_profile_description = 'MPI SHH cluster profile provided by nf-core/configs.'
config_profile_contact = 'James Fellows Yates (@jfy133)' config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_url = 'https://shh.mpg.de' config_profile_url = 'https://shh.mpg.de'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'uct_hex'
config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.' config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.'
config_profile_contact = 'Katie Lennard (@kviljoen)' config_profile_contact = 'Katie Lennard (@kviljoen)'
config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/' config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/'
@ -22,4 +21,3 @@ executor{
executor = 'pbs' executor = 'pbs'
jobName = { "$task.tag" } jobName = { "$task.tag" }
} }

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@ -1,6 +1,5 @@
// Profile config names for nf-core/configs // Profile config names for nf-core/configs
params { params {
config_profile_name = 'UPPMAX-devel'
config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.' config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
config_profile_contact = 'Phil Ewels (@ewels)' config_profile_contact = 'Phil Ewels (@ewels)'
config_profile_url = 'https://www.uppmax.uu.se/' config_profile_url = 'https://www.uppmax.uu.se/'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params { params {
config_profile_name = 'UPPMAX'
config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.' config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.'
config_profile_contact = 'Phil Ewels (@ewels)' config_profile_contact = 'Phil Ewels (@ewels)'
config_profile_url = 'https://www.uppmax.uu.se/' config_profile_url = 'https://www.uppmax.uu.se/'

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@ -1,6 +1,5 @@
//Profile config names for nf-core/configs //Profile config names for nf-core/configs
params{ params{
config_profile_name = 'UZH'
config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_description = 'UZH science cloud profile provided by nf-core/configs'
config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)'
config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html'

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@ -23,9 +23,17 @@ profiles {
phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" }
shh { includeConfig "${params.custom_config_base}/conf/shh.config" } shh { includeConfig "${params.custom_config_base}/conf/shh.config" }
uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" } uct_hex { includeConfig "${params.custom_config_base}/conf/uct_hex.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config" uppmax_devel { includeConfig "${params.custom_config_base}/conf/uppmax.config"; includeConfig "${params.custom_config_base}/conf/uppmax-devel.config" }
includeConfig "${params.custom_config_base}/conf/uppmax-devel.config"
}
uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" } uppmax { includeConfig "${params.custom_config_base}/conf/uppmax.config" }
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 {
// This is a groovy map, not a nextflow parameter set
hostnames = [
uppmax: ['.uppmax.uu.se']
]
}