Change from bytes to string.

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", "wb")
+        macs_file = open("version_macs.txt", "w")
         macs_file.write(macs_version)
         macs_file.close()
 
@@ -99,7 +99,7 @@ def check_tools():
             bg_bw_version = e.output
 
         # Write to file
-        bg_bw_file = open("version_bedGraphToBigWig.txt", "wb")
+        bg_bw_file = open("version_bedGraphToBigWig.txt", "w")
         bg_bw_file.write(bg_bw_version)
         bg_bw_file.close()
     else:

workflow/scripts/convert_reads.py

@@ -60,7 +60,7 @@ def check_tools():
         bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
 
         # Write to file
-        bedtools_file = open("version_bedtools.txt", "wb")
+        bedtools_file = open("version_bedtools.txt", "w")
         bedtools_file.write(bedtools_version)
         bedtools_file.close()
     else:
@@ -76,7 +76,7 @@ def check_tools():
         samtools_version = subprocess.check_output(samtools_version_command, shell=True)
 
         # Write to file
-        samtools_file = open("version_samtools.txt", "wb")
+        samtools_file = open("version_samtools.txt", "w")
         samtools_file.write(samtools_version)
         samtools_file.close()
     else:

workflow/scripts/experiment_qc.py

@@ -58,7 +58,7 @@ def check_tools():
         deeptools_version = subprocess.check_output(deeptools_version_command, shell=True, stderr=subprocess.STDOUT)
 
         # Write to file
-        deeptools_file = open("version_deeptools.txt", "wb")
+        deeptools_file = open("version_deeptools.txt", "w")
         deeptools_file.write(deeptools_version)
         deeptools_file.close()
     else:

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", "wb")
+        samtools_file = open("version_samtools.txt", "w")
         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", "wb")
+        sambamba_file = open("version_sambamba.txt", "w")
         sambamba_file.write(sambamba_version)
         sambamba_file.close()
     else:
@@ -103,7 +103,7 @@ def check_tools():
         bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
 
         # Write to file
-        bedtools_file = open("version_bedtools.txt", "wb")
+        bedtools_file = open("version_bedtools.txt", "w")
         bedtools_file.write(bedtools_version)
         bedtools_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", "wb")
+        bwa_file = open("version_bwa.txt", "w")
         bwa_file.write(bwa_version)
         bwa_file.close()
     else:
@@ -95,7 +95,7 @@ def check_tools():
         samtools_version = subprocess.check_output(samtools_version_command, shell=True)
 
         # Write to file
-        samtools_file = open("version_samtools.txt", "wb")
+        samtools_file = open("version_samtools.txt", "w")
         samtools_file.write(samtools_version)
         samtools_file.close()
     else:

workflow/scripts/motif_search.py

@@ -71,7 +71,7 @@ def check_tools():
         memechip_version = subprocess.check_output(memechip_version_command, shell=True)
 
         # Write to file
-        meme_file = open("version_memechip.txt", "wb")
+        meme_file = open("version_memechip.txt", "w")
         meme_file.write("Version %s" % (memechip_version))
         meme_file.close()
     else:
@@ -87,7 +87,7 @@ def check_tools():
         bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
 
         # Write to file
-        bedtools_file = open("version_bedtools.txt", "wb")
+        bedtools_file = open("version_bedtools.txt", "w")
         bedtools_file.write(bedtools_version)
         bedtools_file.close()
     else:

workflow/scripts/overlap_peaks.py

@@ -56,7 +56,7 @@ def check_tools():
         bedtools_version = subprocess.check_output(bedtools_version_command, shell=True)
 
         # Write to file
-        bedtools_file = open("version_bedtools.txt", "wb")
+        bedtools_file = open("version_bedtools.txt", "w")
         bedtools_file.write(bedtools_version)
         bedtools_file.close()
     else:

workflow/scripts/trim_reads.py

@@ -60,7 +60,7 @@ def check_tools():
         trimgalore_version = subprocess.check_output(trim_version_command, shell=True)
 
         # Write to file
-        trimgalore_file = open("version_trimgalore.txt", "wb")
+        trimgalore_file = open("version_trimgalore.txt", "w")
         trimgalore_file.write(trimgalore_version)
         trimgalore_file.close()
     else:
@@ -76,7 +76,7 @@ def check_tools():
         cutadapt_version = subprocess.check_output(cutadapt_version_command, shell=True)
 
         # Write to file
-        cutadapt_file = open("version_cutadapt.txt", "wb")
+        cutadapt_file = open("version_cutadapt.txt", "w")
         cutadapt_file.write("Version %s" % (cutadapt_version))
         cutadapt_file.close()
     else:

workflow/scripts/xcor.py

@@ -66,7 +66,7 @@ def check_tools():
         r_version = subprocess.check_output(r_version_command, shell=True)
 
         # Write to file
-        r_file = open("version_r.txt", "wb")
+        r_file = open("version_r.txt", "w")
         r_file.write(r_version)
         r_file.close()
     else:
@@ -82,7 +82,7 @@ def check_tools():
         spp_version = subprocess.check_output(spp_version_command, shell=True)
 
         # Write to file
-        spp_file = open("version_spp.txt", "wb")
+        spp_file = open("version_spp.txt", "w")
         spp_file.write(spp_version)
         spp_file.close()
     else: