Merge branch 'master' into config_ucph-mjolnir_ash

README.md

@@ -194,6 +194,8 @@ Currently documentation is available for the following pipelines within specific
   - [UPPMAX](docs/pipeline/ampliseq/uppmax.md)
 - eager
   - [EVA](docs/pipeline/eager/eva.md)
+- mag
+  - [EVA](docs/pipeline/mag/eva.md)
 - rnafusion
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
 - rnavar

conf/hasta.config

@@ -10,6 +10,7 @@ params {
 
 singularity {
   enabled = true
+  envWhitelist = ['_JAVA_OPTIONS']
 }
 
 params {

conf/pipeline/mag/eva.config

@@ -0,0 +1,14 @@
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_description = 'nf-core/mag EVA profile provided by nf-core/configs'
+}
+
+process {
+
+    withName: FASTQC {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+}

conf/pipeline/raredisease/hasta.config

@@ -7,4 +7,7 @@ process {
         cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
         memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
     }
+    withName:'QUALIMAP_BAMQC' {
+        ext.args = { "--java-mem-size=${task.memory.giga / 1.15 as long}G" }
+    }
 }

docs/pipeline/mag/eva.md

@@ -0,0 +1,15 @@
+# nf-core/configs: eva mag specific configuration
+
+Extra specific configuration for mag pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile eva`.
+
+This will download and launch the mag specific [`eva.config`](../../../conf/pipeline/mag/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
+
+Example: `nextflow run nf-core/mag -profile eva`
+
+## mag specific configurations for eva
+
+Specific configurations for eva has been made for mag, primarily adjusting SGE memory requirements of Java tools (e.g. FastQC).

pipeline/mag.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/mag custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/mag folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  eva { includeConfig "${params.custom_config_base}/conf/pipeline/mag/eva.config" }
+}