From 5e62c05a10c58fb4fe63a65ac913955d52ea72d9 Mon Sep 17 00:00:00 2001
From: iquasere <maildosequeira@gmail.com>
Date: Tue, 2 Feb 2021 21:35:52 +0000
Subject: [PATCH] Preprocessing now considers "adapter content" module closes
 #13

---
 workflow/envs/meta.yaml        | 4 ++--
 workflow/mosca.py              | 2 +-
 workflow/scripts/preprocess.py | 6 ++++--
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/workflow/envs/meta.yaml b/workflow/envs/meta.yaml
index 4b86c36..206538d 100644
--- a/workflow/envs/meta.yaml
+++ b/workflow/envs/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "mosca" %}
-{% set version = "1.3.0" %}
+{% set version = "1.3.1" %}
 {% set sha256 = "87cbca039ea9b9c85f417543f2426b2b2acffebe58179878ee6872a32ae949ba" %}
 
 package:
@@ -40,7 +40,7 @@ requirements:
     - svn >=1.9.7
     - reportlab >=3.5.45
     - openpyxl >=3.0.3
-    - xlrd >=0.9.0
+    - xlrd =1.2
     - r-rcolorbrewer >=1.1.2
     - pandas >=1.1.4
     - scikit-learn >=0.23.1
diff --git a/workflow/mosca.py b/workflow/mosca.py
index b19722a..13c0481 100644
--- a/workflow/mosca.py
+++ b/workflow/mosca.py
@@ -6,7 +6,7 @@
 import multiprocessing
 import sys
 
-__version__ = '1.3.0'
+__version__ = '1.3.1'
 
 parser = argparse.ArgumentParser(description="MOSCA's main script")
 parser.add_argument("-s", "--snakefile", type=str, default="{}/Snakefile".format(sys.path[0]), help="Snakefile file")
diff --git a/workflow/scripts/preprocess.py b/workflow/scripts/preprocess.py
index 40f0d3b..c0fa700 100644
--- a/workflow/scripts/preprocess.py
+++ b/workflow/scripts/preprocess.py
@@ -58,8 +58,10 @@ def run_fastqc(self, files, out_dir, extract=True, threads='12'):
 
     def has_adapters(self, fastqc_report):
         data = parse_fastqc(fastqc_report)
-        terms_list = ['Adapter', 'Illumina',
-                      'Primer']  # Terms that appear in FastQC chapter "overrepresented sequences"
+        if not data['Adapter Content'][0] == 'pass':
+            return True
+        terms_list = [
+            'Adapter', 'Illumina', 'Primer']  # Terms that appear in FastQC chapter "overrepresented sequences"
         if not data['Overrepresented sequences'][0] == 'pass':
             i = 0
             while i < len(data['Overrepresented sequences'][1]['Possible Source']):