From e1f780d976d012822a5448537a2981bfc5c2e88f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Thu, 12 May 2022 07:54:17 +0100
Subject: [PATCH] Add taxprofiler for eVA

---
 README.md                            |  6 ++++--
 conf/pipeline/taxprofiler/eva.config | 29 ++++++++++++++++++++++++++++
 docs/pipeline/taxprofiler/eva.md     | 19 ++++++++++++++++++
 pipeline/taxprofiler.config          |  3 +++
 4 files changed, 55 insertions(+), 2 deletions(-)
 create mode 100644 conf/pipeline/taxprofiler/eva.config
 create mode 100644 docs/pipeline/taxprofiler/eva.md
 create mode 100644 pipeline/taxprofiler.config

diff --git a/README.md b/README.md
index 398acca..43b8c71 100644
--- a/README.md
+++ b/README.md
@@ -194,11 +194,13 @@ Currently documentation is available for the following pipelines within specific
   - [EVA](docs/pipeline/eager/eva.md)
 - rnafusion
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
+- rnavar
+  - [MUNIN](docs/pipeline/rnavar/munin.md)
 - sarek
   - [MUNIN](docs/pipeline/sarek/munin.md)
   - [UPPMAX](docs/pipeline/sarek/uppmax.md)
-- rnavar
-  - [MUNIN](docs/pipeline/rnavar/munin.md)
+- taxprofiler
+  - [EVA](docs/pipeline/taxprofiler/eva.md)
 
 ### Pipeline-specific documentation
 
diff --git a/conf/pipeline/taxprofiler/eva.config b/conf/pipeline/taxprofiler/eva.config
new file mode 100644
index 0000000..59b5fc6
--- /dev/null
+++ b/conf/pipeline/taxprofiler/eva.config
@@ -0,0 +1,29 @@
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_description = 'nf-core/taxprofiler EVA profile provided by nf-core/configs'
+}
+
+process {
+
+    withName: BBMAP_BBDUK {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+    withName: MALT_RUN {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+    withName: METAPHLAN3 {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+    withName: MEGAN_RMA2INFO {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+}
diff --git a/docs/pipeline/taxprofiler/eva.md b/docs/pipeline/taxprofiler/eva.md
new file mode 100644
index 0000000..fc7e3d8
--- /dev/null
+++ b/docs/pipeline/taxprofiler/eva.md
@@ -0,0 +1,19 @@
+# nf-core/configs: eva taxprofiler specific configuration
+
+Extra specific configuration for taxprofiler pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile eva`.
+
+This will download and launch the taxprofiler specific [`eva.config`](../../../conf/pipeline/taxprofiler/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
+
+Example: `nextflow run nf-core/taxprofiler -profile eva`
+
+## taxprofiler specific configurations for eva
+
+Specific configurations for eva has been made for taxprofiler.
+
+### General profiles
+
+- The general MPI-EVA profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues SGE have with Java and python tools, nameling: BBDUK, MALT, MetaPhlAn3, and MEGAN
diff --git a/pipeline/taxprofiler.config b/pipeline/taxprofiler.config
new file mode 100644
index 0000000..f9eea2d
--- /dev/null
+++ b/pipeline/taxprofiler.config
@@ -0,0 +1,3 @@
+profiles {
+  eva { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/eva.config" }
+}