Update byte output and conf.

workflow/conf/biohpc.config

@@ -61,7 +61,7 @@ process {
     cpus = 32
   }
   withName: softwareReport {
-    module = ['python/3.6.1-2-anaconda']
+    module = ['python/3.6.1-2-anaconda', 'pandoc/2.7']
     executor = 'local'
   }
 }

workflow/scripts/call_peaks_macs.py

@@ -79,7 +79,7 @@ def check_tools():
         macs_version = subprocess.check_output(macs_version_command, shell=True, stderr=subprocess.STDOUT)
 
         # Write to file
-        macs_file = open("version_macs.txt", "w")
+        macs_file = open("version_macs.txt", "wb")
         macs_file.write(macs_version)
         macs_file.close()
 

workflow/scripts/map_qc.py

@@ -68,7 +68,7 @@ def check_tools():
         samtools_version = subprocess.check_output(samtools_version_command, shell=True)
 
         # Write to file
-        samtools_file = open("version_samtools.txt", "w")
+        samtools_file = open("version_samtools.txt", "wb")
         samtools_file.write(samtools_version)
         samtools_file.close()
     else:
@@ -87,7 +87,7 @@ def check_tools():
             sambamba_version = e.output
 
         # Write to file
-        sambamba_file = open("version_sambamba.txt", "w")
+        sambamba_file = open("version_sambamba.txt", "wb")
         sambamba_file.write(sambamba_version)
         sambamba_file.close()
     else:

workflow/scripts/map_reads.py

@@ -79,7 +79,7 @@ def check_tools():
             bwa_version = e.output
 
         # Write to file
-        bwa_file = open("version_bwa.txt", "w")
+        bwa_file = open("version_bwa.txt", "wb")
         bwa_file.write(bwa_version)
         bwa_file.close()
     else:

workflow/scripts/motif_search.py

@@ -71,8 +71,8 @@ def check_tools():
         memechip_version = subprocess.check_output(memechip_version_command, shell=True)
 
         # Write to file
-        meme_file = open("version_memechip.txt", "w")
-        meme_file.write("Version %s" % (memechip_version))
+        meme_file = open("version_memechip.txt", "wb")
+        meme_file.write(b"Version %s" % (memechip_version))
         meme_file.close()
     else:
         logger.error('Missing meme')

workflow/scripts/trim_reads.py

@@ -77,7 +77,7 @@ def check_tools():
 
         # Write to file
         cutadapt_file = open("version_cutadapt.txt", "wb")
-        cutadapt_file.write("Version %s" % (cutadapt_version))
+        cutadapt_file.write(b"Version %s" % (cutadapt_version))
         cutadapt_file.close()
     else:
         logger.error('Missing cutadapt')