millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-24 00:59:55 +00:00
Code Issues Releases Packages Activity

Adding UPPMAX specific config for ampliseq

Browse source
This commit is contained in:
Daniel Lundin 2020-03-31 15:17:24 +02:00
parent 15574ab849
commit c8de9be701
3 changed files with 37 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

15
conf/pipeline/ampliseq/uppmax.config Normal file
View file

@ -0,0 +1,15 @@
// Profile config names for nf-core/configs
params {
// Specific nf-core/configs params
config_profile_contact = 'Daniel Lundin (daniel.lundin@lnu.se)'
config_profile_description = 'nf-core/ampliseq UPPMAX profile provided by nf-core/configs'
}
withName: make_SILVA_132_16S_classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}
withName: classifier {
clusterOptions = { "-A $params.project -C fat -p node -N 1 ${params.clusterOptions ?: ''}" }
}

17
docs/pipeline/ampliseq/uppmax.md Normal file
View file

@ -0,0 +1,17 @@
# nf-core/configs: uppmax ampliseq specific configuration
Extra specific configuration for the ampliseq pipeline.
## Usage
To use, run the pipeline with `-profile uppmax`.
This will download and launch the ampliseq specific [`uppmax.config`](../../../conf/pipeline/ampliseq/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX cluster.
Example: `nextflow run nf-core/ampliseq -profile uppmax`
## ampliseq specific configurations for uppmax
Specific configurations for UPPMAX has been made for ampliseq.
* Makes sure that a fat node is allocated for training and applying a Bayesian classifier.

6
pipeline/ampliseq.config
View file

@ -10,4 +10,8 @@
profiles {
binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
}
}
profiles {
uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" }
}