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Merge pull request #57 from marchoeppner/dev

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Adding CCGA DX cluster config
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Harshil Patel 2019-07-29 13:13:13 +02:00 committed by GitHub
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1
README.md
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@ -85,6 +85,7 @@ Currently documentation is available for the following clusters:
* [BINAC](docs/binac.md)
* [BIGPURPLE](docs/bigpurple.md)
* [CCGA](docs/ccga.md)
* [CCGA_DX](/docs/ccga_dx.md)
* [CFC](docs/binac.md)
* [CRICK](docs/crick.md)
* [GIS](docs/gis.md)

37
conf/ccga_dx.config Normal file
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@ -0,0 +1,37 @@
//Profile config names for nf-core/configs
params {
config_profile_description = 'CCGA DX cluster profile provided by nf-core/configs.'
config_profile_contact = 'Marc Hoeppner (@marchoeppner)'
config_profile_url = 'https://www.ccga.uni-kiel.de/'
}
/*
* -------------------------------------------------
* Nextflow config file for CCGA cluster in Kiel
* -------------------------------------------------
*/
singularity {
enabled = true
}
executor {
queueSize=100
}
process {
// Global process config
executor = 'slurm'
queue = 'htc'
}
params {
// illumina iGenomes reference file paths on DX Cluster
igenomes_base = '/mnt/ld_ng_out/sukmb352/references/iGenomes/references/'
saveReference = true
max_memory = 250.GB
max_cpus = 20
max_time = 240.h
}

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docs/ccga_dx.md Normal file
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@ -0,0 +1,9 @@
# nf-core/configs: CCGA DX Configuration
Deployment and testing of nf-core pipelines at the CCGA DX cluster is on-going.
To use, run the pipeline with `-profile ccga_dx`. This will download and launch the [`ccga_dx.config`](../conf/ccga_dx.config) which has been pre-configured with a setup suitable for the CCGA cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to have Nextflow installed.
>NB: Access to the CCGA DX cluster is restricted to IKMB/CCGA employes. Please talk to Marc Hoeppner to get access (@marchoeppner).

1
nfcore_custom.config
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@ -14,6 +14,7 @@ params.custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/$
profiles {
binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
ccga { includeConfig "${params.custom_config_base}/conf/ccga.config" }
ccga_dx { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
cfc { includeConfig "${params.custom_config_base}/conf/cfc.config" }
crick { includeConfig "${params.custom_config_base}/conf/crick.config" }
czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }