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Adjust general usage to separate params section

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This commit is contained in:
Alexander Peltzer 2019-01-04 14:55:22 +01:00
parent 9c97680d4c
commit 7af6b48b4d
7 changed files with 50 additions and 91 deletions
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20
conf/binac.config
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@ -1,11 +1,10 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------------------- params {
* Name: BINAC config_profile_name = 'BINAC'
* Description: Configuration profile for BinAC clusters in Baden-Wuerttemberg/Germany. config_profile_description = 'BINAC Cluster Profile provided by nf-core/configs.'
* Contact person: Alexander Peltzer (@apeltzer) config_profile_contact = 'Alexander Peltzer (@apeltzer)'
* 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'
* ------------------------------------------------------------- }
*/
singularity { singularity {
enabled = true enabled = true
@ -22,9 +21,4 @@ params {
max_memory = 128.GB max_memory = 128.GB
max_cpus = 28 max_cpus = 28
max_time = 48.h max_time = 48.h
config_profile_name = 'BINAC'
config_profile_description = 'BINAC Cluster Profile provided by nf-core/configs.'
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'https://www.bwhpc-c5.de/wiki/index.php/Category:BwForCluster_BinAC'
} }

20
conf/cfc.config
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@ -1,11 +1,10 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------------------- params {
* Name: CFC config_profile_name = 'CFC'
* Description: Core Facility Cluster Profile provided by nf-core/configs. config_profile_description = 'Core Facility Cluster Profile provided by nf-core/configs.'
* Contact person: Alexander Peltzer (@apeltzer) config_profile_contact = 'Alexander Peltzer (@apeltzer)'
* URL: http://qbic.uni-tuebingen.de/ config_profile_url = 'http://qbic.uni-tuebingen.de/'
* ------------------------------------------------------------- }
*/
singularity { singularity {
enabled = true enabled = true
@ -21,9 +20,4 @@ params {
max_memory = 60.GB max_memory = 60.GB
max_cpus = 24 max_cpus = 24
max_time = 140.h max_time = 140.h
config_profile_name = 'CFC'
config_profile_description = 'Core Facility Cluster Profile provided by nf-core/configs.'
config_profile_contact = 'Alexander Peltzer (@apeltzer)'
config_profile_url = 'http://qbic.uni-tuebingen.de/'
} }

7
conf/crick.config
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@ -3,6 +3,13 @@
* Nextflow config file for CAMP HPC @ The Crick * Nextflow config file for CAMP HPC @ The Crick
* ------------------------------------------------- * -------------------------------------------------
*/ */
//Profile config names for nf-core/configs
params {
config_profile_name = 'CRICK'
config_profile_description = 'CAMP HPC @ The Crick Cluster Profile provided by nf-core/configs.'
config_profile_contact = 'Harshil Patel (@drpatelh )'
config_profile_url = 'https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies'
}
singularity { singularity {
enabled = true enabled = true

28
conf/mendel.config
View file

@ -1,19 +1,10 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------------------- params {
* Name: CFC config_profile_name = 'MENDEL'
* Description: MENDEL cluster profile provided by nf-core/configs config_profile_description = 'MENDEL cluster profile provided by nf-core/configs'
* Contact person: Philipp H (@phue) config_profile_contact = 'Philipp H (@phue)'
* URL: http://www.gmi.oeaw.ac.at/ config_profile_url = 'http://www.gmi.oeaw.ac.at/'
* ------------------------------------------------------------- }
*/
/*
* --------------------------------------------------------------------------------------
* Nextflow config file for the MENDEL cluster at the Gregor Mendel Institute in Vienna
* -------------------------------------------------------------------------------------
*/
phue
singularity { singularity {
enabled = true enabled = true
@ -28,9 +19,4 @@ process {
params { params {
max_time = 192.h max_time = 192.h
igenomesIgnore = true igenomesIgnore = true
config_profile_name = 'MENDEL'
config_profile_description = 'MENDEL cluster profile provided by nf-core/configs'
config_profile_contact = 'Philipp H (@phue)'
config_profile_url = 'http://www.gmi.oeaw.ac.at/'
} }

20
conf/phoenix.config
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@ -1,11 +1,10 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------------------- params {
* Name: PHOENIX config_profile_name = 'PHOENIX'
* Description: Phoenix Research cluster profile provided by nf-core/configs config_profile_description = 'Phoenix Research cluster profile provided by nf-core/configs'
* Contact person: Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer) config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)'
* URL: https://www.adelaide.edu.au/phoenix/ config_profile_url = 'https://www.adelaide.edu.au/phoenix/'
* ------------------------------------------------------------- }
*/
singularity { singularity {
enabled = true enabled = true
@ -22,9 +21,4 @@ params {
max_memory = 128.GB max_memory = 128.GB
max_cpus = 32 max_cpus = 32
max_time = 48.h max_time = 48.h
config_profile_name = 'PHOENIX'
config_profile_description = 'Phoenix Research cluster profile provided by nf-core/configs'
config_profile_contact = 'Yassine Souilmi / Alexander Peltzer (@yassineS, @apeltzer)'
config_profile_url = 'https://www.adelaide.edu.au/phoenix/'
} }

25
conf/shh.config
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@ -1,34 +1,23 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------------------- params {
* Name: SHH config_profile_name = 'SHH'
* Description: Configuration profile for MPI SHH Jena clusters. config_profile_description = 'MPI SHH Cluster Profile provided by nf-core/configs.'
* Contact person: James Fellows Yates (@jfy133) config_profile_contact = 'James Fellows Yates (@jfy133)'
* URL: https://shh.mpg.de config_profile_url = 'https://shh.mpg.de'
* ------------------------------------------------------------- }
*/
singularity { singularity {
enabled = true enabled = true
cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/" cacheDir = "/projects1/users/$USER/nextflow/nf_cache/singularity/"
} }
/*
* To be improved by process specific resource requests
* By default, take the medium queue, smaller processes might just go to short (e.g. multiqc or similar things)
*/
process { process {
executor = 'slurm' executor = 'slurm'
queue = 'medium' queue = 'medium'
} }
params { params {
max_memory = 734.GB max_memory = 734.GB
max_cpus = 64 max_cpus = 64
max_time = 48.h max_time = 48.h
config_profile_name = 'SHH'
config_profile_description = 'MPI SHH Cluster Profile provided by nf-core/configs.'
config_profile_contact = 'James Fellows Yates (@jfy133)'
config_profile_url = 'https://shh.mpg.de'
} }

21
conf/uzh.config
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@ -1,11 +1,11 @@
/* //Profile config names for nf-core/configs
* ------------------------------------------------------------- params{
* Name: UZH config_profile_name = 'UZH'
* Description: UZH science cloud profile provided by nf-core/configs config_profile_description = 'UZH science cloud profile provided by nf-core/configs'
* Contact person: Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer) config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)'
* URL: https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html'
* ------------------------------------------------------------- }
*/
singularity { singularity {
enabled = true enabled = true
} }
@ -18,9 +18,4 @@ params {
max_memory = 1800.GB max_memory = 1800.GB
max_cpus = 112 max_cpus = 112
max_time = 168.h max_time = 168.h
config_profile_name = 'UZH'
config_profile_description = 'UZH science cloud profile provided by nf-core/configs'
config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)'
config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html'
} }