diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 07407ef8c8d5c3b4f34f0ade0b9ff2c8d78b69ce..739fce695526dc7434cd5cbc0b42c38e4ed32bd1 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -60,7 +60,14 @@ process {
module = ['python/3.6.1-2-anaconda', 'meme/4.11.1-gcc-openmpi', 'bedtools/2.26.0']
cpus = 32
}
-
+ withName: softwareVersions {
+ module = ['python/3.6.1-2-anaconda']
+ executor = 'local'
+ }
+ withName: softwareReport {
+ module = ['python/3.6.1-2-anaconda']
+ executor = 'local'
+ }
}
params {
diff --git a/workflow/main.nf b/workflow/main.nf
index ceed1c12bc6a9dd939199e32e7197bffc6df8db2..513c4b55164881a06eb256de0e79d766352fd973 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -47,6 +47,7 @@ cutoffRatio = params.cutoffRatio
outDir = params.outDir
extendReadsLen = params.extendReadsLen
topPeakCount = params.topPeakCount
+references = params.references
// Check design file for errors
process checkDesignFile {
@@ -478,7 +479,7 @@ process diffPeaks {
}
// Collect Software Versions and references
-process softwareVersions {
+process softwareReport {
input:
@@ -495,10 +496,12 @@ process softwareVersions {
experimentQCVersions
output:
- file 'software_versions_mqc.yaml' into softwareVersions
+ file '*_mqc.yaml' into softwareVersions
+ file '*_mqc.yaml' into softwareReferences
script:
"""
- software_report.py > software_versions_mqc.yaml
+ python3 $baseDir/scripts/software_report.py -o software_versions
+ python3 $baseDir/scripts/generate_references.py -r $references -o software_references
"""
}
diff --git a/workflow/scripts/software_report.py b/workflow/scripts/software_report.py
index 5f9abe1aed34ba27b9d5aba0ed334533497a554a..2823bcef1518ed511a68faf215b818a65f14f7a1 100644
--- a/workflow/scripts/software_report.py
+++ b/workflow/scripts/software_report.py
@@ -6,9 +6,22 @@
from __future__ import print_function
from collections import OrderedDict
import re
+import logging
+import argparse
+EPILOG = '''
+For more details:
+ %(prog)s --help
+'''
-software_regex = {
+# SETTINGS
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+logger.setLevel(logging.INFO)
+
+SOFTWARE_REGEX = {
'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
'Cutadapt': ['version_cutadapt.txt', r"Version (\S+)"],
'BWA': ['version_bwa.txt', r"Version: (\S+)"],
@@ -25,45 +38,72 @@ software_regex = {
'deepTools': ['version_deeptools.txt', r"deeptools (\S+)"],
}
-results = OrderedDict()
-results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
-results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
-results['BWA'] = '<span style="color:#999999;\">N/A</span>'
-results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
-results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
-results['BWA'] = '<span style="color:#999999;\">N/A</span>'
-results['Samtools'] = '<span style="color:#999999;\">N/A</span>'
-results['Sambamba'] = '<span style="color:#999999;\">N/A</span>'
-results['BEDTools'] = '<span style="color:#999999;\">N/A</span>'
-results['R'] = '<span style="color:#999999;\">N/A</span>'
-results['SPP'] = '<span style="color:#999999;\">N/A</span>'
-results['MACS2'] = '<span style="color:#999999;\">N/A</span>'
-results['bedGraphToBigWig'] = '<span style="color:#999999;\">N/A</span>'
-results['ChIPseeker'] = '<span style="color:#999999;\">N/A</span>'
-results['MEME-ChIP'] = '<span style="color:#999999;\">N/A</span>'
-results['DiffBind'] = '<span style="color:#999999;\">N/A</span>'
-results['deepTools'] = '<span style="color:#999999;\">N/A</span>'
-
-# Search each file using its regex
-for k, v in software_regex.items():
- with open(v[0]) as x:
- versions = x.read()
- match = re.search(v[1], versions)
- if match:
- results[k] = "v{}".format(match.group(1))
-
-# Dump to YAML
-print(
- '''
- id: 'Software Versions'
- section_name: 'Software Versions'
- section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
- plot_type: 'html'
- description: 'are collected at run time from the software output.'
- data: |
- <dl class="dl-horizontal">
- '''
-)
-for k, v in results.items():
- print(" <dt>{}</dt><dd>{}</dd>".format(k, v))
-print(" </dl>")
+
+def get_args():
+ '''Define arguments.'''
+
+ parser = argparse.ArgumentParser(
+ description=__doc__, epilog=EPILOG,
+ formatter_class=argparse.RawDescriptionHelpFormatter)
+
+ parser.add_argument('-o', '--output',
+ help="The out file name.",
+ required=True)
+
+ args = parser.parse_args()
+ return args
+
+
+def main():
+ args = get_args()
+ output = args.output
+
+ out_filename = output + '_mqc.yaml'
+
+ results = OrderedDict()
+ results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
+ results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
+ results['BWA'] = '<span style="color:#999999;\">N/A</span>'
+ results['Trim Galore!'] = '<span style="color:#999999;\">N/A</span>'
+ results['Cutadapt'] = '<span style="color:#999999;\">N/A</span>'
+ results['BWA'] = '<span style="color:#999999;\">N/A</span>'
+ results['Samtools'] = '<span style="color:#999999;\">N/A</span>'
+ results['Sambamba'] = '<span style="color:#999999;\">N/A</span>'
+ results['BEDTools'] = '<span style="color:#999999;\">N/A</span>'
+ results['R'] = '<span style="color:#999999;\">N/A</span>'
+ results['SPP'] = '<span style="color:#999999;\">N/A</span>'
+ results['MACS2'] = '<span style="color:#999999;\">N/A</span>'
+ results['bedGraphToBigWig'] = '<span style="color:#999999;\">N/A</span>'
+ results['ChIPseeker'] = '<span style="color:#999999;\">N/A</span>'
+ results['MEME-ChIP'] = '<span style="color:#999999;\">N/A</span>'
+ results['DiffBind'] = '<span style="color:#999999;\">N/A</span>'
+ results['deepTools'] = '<span style="color:#999999;\">N/A</span>'
+
+ # Search each file using its regex
+ for k, v in SOFTWARE_REGEX.items():
+ with open(v[0]) as x:
+ versions = x.read()
+ match = re.search(v[1], versions)
+ if match:
+ results[k] = "v{}".format(match.group(1))
+
+ # Dump to YAML
+ print(
+ '''
+ id: 'Software Versions'
+ section_name: 'Software Versions'
+ section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
+ plot_type: 'html'
+ description: 'are collected at run time from the software output.'
+ data: |
+ <dl class="dl-horizontal">
+ '''
+ , file = open(out_filename, "w"))
+
+ for k, v in results.items():
+ print(" <dt>{}</dt><dd>{}</dd>".format(k, v), file = open(out_filename, "a"))
+ print(" </dl>", file = open(out_filename, "a"))
+
+
+if __name__ == '__main__':
+ main()