From ed10bb9d2ad4c758b7157b25a16d157cfbc6259d Mon Sep 17 00:00:00 2001
From: Harshil Patel <drpatelhh@gmail.com>
Date: Sun, 2 Oct 2022 11:48:10 +0100
Subject: [PATCH] Fix linting

---
 bin/igv_files_to_session.py | 13 +++----------
 modules/local/igv.nf        |  4 ++--
 2 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/bin/igv_files_to_session.py b/bin/igv_files_to_session.py
index 08e5adf9..629e6cc9 100755
--- a/bin/igv_files_to_session.py
+++ b/bin/igv_files_to_session.py
@@ -17,9 +17,7 @@
 ############################################
 
 Description = 'Create IGV session file from a list of files and associated colours - ".bed", ".bw", ".bigwig", ".tdf", ".gtf" files currently supported.'
-Epilog = (
-    """Example usage: python igv_files_to_session.py <XML_OUT> <LIST_FILE> <GENOME>"""
-)
+Epilog = """Example usage: python igv_files_to_session.py <XML_OUT> <LIST_FILE> <GENOME>"""
 
 argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
 
@@ -109,10 +107,7 @@ def igv_files_to_session(XMLOut, ListFile, ReplaceFile, Genome, PathPrefix=""):
 
     ## ADD RESOURCES SECTION
     XMLStr = '<?xml version="1.0" encoding="UTF-8" standalone="no"?>\n'
-    XMLStr += (
-        '<Session genome="%s" hasGeneTrack="true" hasSequenceTrack="true" locus="All" version="8">\n'
-        % (Genome)
-    )
+    XMLStr += '<Session genome="%s" hasGeneTrack="true" hasSequenceTrack="true" locus="All" version="8">\n' % (Genome)
     XMLStr += "\t<Resources>\n"
     for ifile, colour in fileList:
         XMLStr += '\t\t<Resource path="%s"/>\n' % (ifile)
@@ -149,9 +144,7 @@ def igv_files_to_session(XMLOut, ListFile, ReplaceFile, Genome, PathPrefix=""):
                 '\t\t<Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="%s" '
                 % (colour)
             )
-            XMLStr += (
-                'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" '
-            )
+            XMLStr += 'displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" '
             XMLStr += (
                 'id="%s" name="%s" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count"/>\n'
                 % (ifile, os.path.basename(ifile))
diff --git a/modules/local/igv.nf b/modules/local/igv.nf
index 137abbb4..213904b3 100644
--- a/modules/local/igv.nf
+++ b/modules/local/igv.nf
@@ -16,7 +16,7 @@ process IGV {
     path ("${aligner_dir}/mergedLibrary/macs2/${peak_dir}/*")
     path ("${aligner_dir}/mergedLibrary/macs2/${peak_dir}/consensus/*")
     path ("mappings/*")
-    
+
     output:
     path "*files.txt"  , emit: txt
     path "*.xml"       , emit: xml
@@ -34,7 +34,7 @@ process IGV {
     if [ -d "mappings" ]; then
         cat mappings/* > replace_paths.txt
     fi
-    
+
     cat *.igv.txt > igv_files_orig.txt
     igv_files_to_session.py igv_session.xml igv_files_orig.txt replace_paths.txt ../../genome/${fasta.getName()} --path_prefix '../../'