From 6c5033e805a4dbd02c3a179267ff2401b94b13cb Mon Sep 17 00:00:00 2001
From: Natalia Zajac <natalia.zajac@fgcz.ethz.ch>
Date: Wed, 8 Jun 2022 15:35:22 +0200
Subject: [PATCH] MetagenomeAtlas

---
 master/lib/MetagenomeAtlasApp.rb | 48 ++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 master/lib/MetagenomeAtlasApp.rb

diff --git a/master/lib/MetagenomeAtlasApp.rb b/master/lib/MetagenomeAtlasApp.rb
new file mode 100644
index 000000000..a156f2bfd
--- /dev/null
+++ b/master/lib/MetagenomeAtlasApp.rb
@@ -0,0 +1,48 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+require 'sushi_fabric'
+require_relative 'global_variables'
+include GlobalVariables
+
+class MetagenomeAtlasApp < SushiFabric::SushiApp
+   def initialize
+    super
+    @name = 'MetagenomeAtlasApp'
+    @analysis_category = 'Metagenomics'
+    @description =<<-EOS
+    Data preprocssing with Metagenome Atlas. The input is short reads, requires both R1 and R2 reads and assembles genomes found in the sample.
+    <a href='https://github.com/metagenome-atlas/atlas'>Metagenome Atlas main repository.</a>
+EOS
+    @params['process_mode'] = 'DATASET'
+    @required_columns = ['Name', 'Read1', 'Read2']
+    @required_params = ['paired']    
+    @params['cores'] = '8'
+    @params['paired'] = 'True'
+    @params['paired', 'description'] = 'whether the reads are paired end; if false then only Read1 is considered even if Read2 is available.'
+    @params['ram'] = '60'
+    @params['scratch'] = '60'
+    @params['mail'] = ""
+    @params['name'] = "MetagenomeAtlas"
+    @inherit_tags = ['B-Fabric']
+    @modules = ['Dev/R', 'QC/mash/2.3' , 'QC/fastANI/1.32']
+  end
+
+def next_dataset
+    report_file = File.join(@result_dir, @params['name'])
+    report_link = File.join(report_file, '00index.html')
+    {'Name'=>@params['name'],
+     'Static Report [Link]'=>report_link,
+     'Report [File]'=>report_file,
+    }    
+end
+  def commands
+     run_RApp("EzAppMetagenomeAtlas", conda_env: "metagenome-atlas")
+  end
+end
+
+if __FILE__ == $0
+
+end
+
+