Merge pull request #380 from jfy133/taxprofiler

Add MAG @ EVA profile

README.md

@@ -193,6 +193,8 @@ 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/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' }
+    }
+
+}

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" }
+}