Skip to content
Snippets Groups Projects
Commit 562c52bc authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update byte output and conf.

parent de9c71ea
1 merge request!23Resolve "Output software versions and methods and references"
...@@ -61,7 +61,7 @@ process { ...@@ -61,7 +61,7 @@ process {
cpus = 32 cpus = 32
} }
withName: softwareReport { withName: softwareReport {
module = ['python/3.6.1-2-anaconda'] module = ['python/3.6.1-2-anaconda', 'pandoc/2.7']
executor = 'local' executor = 'local'
} }
} }
......
...@@ -79,7 +79,7 @@ def check_tools(): ...@@ -79,7 +79,7 @@ def check_tools():
macs_version = subprocess.check_output(macs_version_command, shell=True, stderr=subprocess.STDOUT) macs_version = subprocess.check_output(macs_version_command, shell=True, stderr=subprocess.STDOUT)
# Write to file # Write to file
macs_file = open("version_macs.txt", "w") macs_file = open("version_macs.txt", "wb")
macs_file.write(macs_version) macs_file.write(macs_version)
macs_file.close() macs_file.close()
......
...@@ -68,7 +68,7 @@ def check_tools(): ...@@ -68,7 +68,7 @@ def check_tools():
samtools_version = subprocess.check_output(samtools_version_command, shell=True) samtools_version = subprocess.check_output(samtools_version_command, shell=True)
# Write to file # Write to file
samtools_file = open("version_samtools.txt", "w") samtools_file = open("version_samtools.txt", "wb")
samtools_file.write(samtools_version) samtools_file.write(samtools_version)
samtools_file.close() samtools_file.close()
else: else:
...@@ -87,7 +87,7 @@ def check_tools(): ...@@ -87,7 +87,7 @@ def check_tools():
sambamba_version = e.output sambamba_version = e.output
# Write to file # Write to file
sambamba_file = open("version_sambamba.txt", "w") sambamba_file = open("version_sambamba.txt", "wb")
sambamba_file.write(sambamba_version) sambamba_file.write(sambamba_version)
sambamba_file.close() sambamba_file.close()
else: else:
......
...@@ -79,7 +79,7 @@ def check_tools(): ...@@ -79,7 +79,7 @@ def check_tools():
bwa_version = e.output bwa_version = e.output
# Write to file # Write to file
bwa_file = open("version_bwa.txt", "w") bwa_file = open("version_bwa.txt", "wb")
bwa_file.write(bwa_version) bwa_file.write(bwa_version)
bwa_file.close() bwa_file.close()
else: else:
......
...@@ -71,8 +71,8 @@ def check_tools(): ...@@ -71,8 +71,8 @@ def check_tools():
memechip_version = subprocess.check_output(memechip_version_command, shell=True) memechip_version = subprocess.check_output(memechip_version_command, shell=True)
# Write to file # Write to file
meme_file = open("version_memechip.txt", "w") meme_file = open("version_memechip.txt", "wb")
meme_file.write("Version %s" % (memechip_version)) meme_file.write(b"Version %s" % (memechip_version))
meme_file.close() meme_file.close()
else: else:
logger.error('Missing meme') logger.error('Missing meme')
......
...@@ -77,7 +77,7 @@ def check_tools(): ...@@ -77,7 +77,7 @@ def check_tools():
# Write to file # Write to file
cutadapt_file = open("version_cutadapt.txt", "wb") 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() cutadapt_file.close()
else: else:
logger.error('Missing cutadapt') logger.error('Missing cutadapt')
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment