From 3085339385a14eeddb0bb4e5ebb236a4ab494e41 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 11 Mar 2019 17:43:41 -0500
Subject: [PATCH] Update software report and generate references.
---
workflow/main.nf | 4 +-
workflow/scripts/generate_references.py | 66 +++++++++++++++++++++++++
workflow/scripts/software_report.py | 1 +
3 files changed, 70 insertions(+), 1 deletion(-)
create mode 100644 workflow/scripts/generate_references.py
diff --git a/workflow/main.nf b/workflow/main.nf
index ddeb067..ceed1c1 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -17,6 +17,8 @@ params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
params.topPeakCount = 600
+params.references = "$baseDir/../docs/references.md"
+
// Check inputs
if( params.bwaIndex ){
@@ -475,7 +477,7 @@ process diffPeaks {
"""
}
-// Collect Software Versions
+// Collect Software Versions and references
process softwareVersions {
input:
diff --git a/workflow/scripts/generate_references.py b/workflow/scripts/generate_references.py
new file mode 100644
index 0000000..0b7582f
--- /dev/null
+++ b/workflow/scripts/generate_references.py
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+
+'''Make header for HTML of references.'''
+
+import argparse
+import subprocess
+import shlex
+import logging
+
+EPILOG = '''
+For more details:
+ %(prog)s --help
+'''
+
+# SETTINGS
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+logger.setLevel(logging.INFO)
+
+
+def get_args():
+ '''Define arguments.'''
+
+ parser = argparse.ArgumentParser(
+ description=__doc__, epilog=EPILOG,
+ formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument('-r', '--reference',
+ help="The reference file (markdown format).",
+ required=True)
+
+ parser.add_argument('-o', '--output',
+ help="The out file name.",
+ default='references')
+
+ args = parser.parse_args()
+ return args
+
+
+def main():
+ args = get_args()
+ reference = args.reference
+ output = args.output
+
+ out_filename = output + '_mqc.txt'
+
+ # Header for HTML
+ print('''
+ # id: 'References'
+ # section_name: 'References'
+ # description: 'This section describes references for the tools used.'
+ # plot_type: 'html'
+ '''
+ , file = open(out_filename, "w")
+ )
+
+ # Turn Markdown into HTML
+ references_html = 'bash -c "pandoc {} >> {}"'
+ references_html = references_html.format(reference, out_filename)
+ subprocess.check_call(shlex.split(references_html))
+
+
+if __name__ == '__main__':
+ main()
diff --git a/workflow/scripts/software_report.py b/workflow/scripts/software_report.py
index 2e605e3..5f9abe1 100644
--- a/workflow/scripts/software_report.py
+++ b/workflow/scripts/software_report.py
@@ -7,6 +7,7 @@ from __future__ import print_function
from collections import OrderedDict
import re
+
software_regex = {
'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
'Cutadapt': ['version_cutadapt.txt', r"Version (\S+)"],
--
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