Merge pull request #145 from bioatlas/master

Adding UPPMAX specific config for ampliseq

README.md

@@ -165,6 +165,7 @@ Currently documentation is available for the following pipeline within the speci
 
 * ampliseq
   * [BINAC](docs/pipeline/ampliseq/binac.md)
+  * [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
 * eager
   * [SHH](docs/pipeline/eager/shh.md)
 * rnafusion

conf/pipeline/ampliseq/uppmax.config

@@ -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 ?: ''}" }
+}

docs/pipeline/ampliseq/uppmax.md

@@ -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.

pipeline/ampliseq.config

@@ -10,4 +10,5 @@
 
 profiles {
   binac { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/binac.config" }
+  uppmax { includeConfig "${params.custom_config_base}/conf/pipeline/ampliseq/uppmax.config" }
 }