Commit db446d7d authored by aknecht2's avatar aknecht2
Browse files

Updated conf to include excel files. Added new output files to macs2 job & module.

parent 47190424
...@@ -47,7 +47,8 @@ file_extensions = { ...@@ -47,7 +47,8 @@ file_extensions = {
"quality": ["quality"], "quality": ["quality"],
"qc": ["qc"], "qc": ["qc"],
"pdf": ["pdf"], "pdf": ["pdf"],
"ccscore": ["ccscore"] "ccscore": ["ccscore"],
"xls": ["xls"]
} }
# list of resources that can be specified per job (step) in # list of resources that can be specified per job (step) in
......
...@@ -49,7 +49,11 @@ peak_call: ...@@ -49,7 +49,11 @@ peak_call:
type: argument type: argument
additional_inputs: null additional_inputs: null
outputs: outputs:
- results.narrowPeak: - peaks.narrowPeak:
type: file
- peaks.xls:
type: file
- summits.bed:
type: file type: file
- sort_awk_sort_peaks: - sort_awk_sort_peaks:
inputs: inputs:
......
...@@ -10,6 +10,10 @@ macs2_callpeak: ...@@ -10,6 +10,10 @@ macs2_callpeak:
outputs: outputs:
- bed: - bed:
type: file type: file
- xls:
type: file
- bed:
type: file
command: macs2 command: macs2
arguments: arguments:
- callpeak: - callpeak:
......
...@@ -5,8 +5,15 @@ parser = argparse.ArgumentParser(description="Insert a bed file into the databas ...@@ -5,8 +5,15 @@ parser = argparse.ArgumentParser(description="Insert a bed file into the databas
parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.") parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.") parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
parser.add_argument("-h", "--host", dest="host", required=True, help="Database host.") parser.add_argument("-h", "--host", dest="host", required=True, help="Database host.")
parser.add_argument("-f", "--file", dest="file", required=True, help="Path to bed file.") parser.add_argument("-f", "--file", dest="file", required=True, help="Path to result file.")
parser.add_argument("-c", "--controls", dest="control_ids", required=True, nargs="+", help="List of control ids.") parser.add_argument("-c", "--controls", dest="control_ids", required=True, nargs="+", help="List of control ids.")
parser.add_argument("-e", "--experiments", dest="experiment_ids", required=True, nargs="+", help="List of experiment/signal ids.") parser.add_argument("-e", "--experiments", dest="experiment_ids", required=True, nargs="+", help="List of experiment/signal ids.")
parser.add_argument("-a", "--additional", dest="additional") parser.add_argument("-a", "--additional", dest="additional")
parser.add_argument("-t", "--type", dest="type", required=True, help="Type of result file to save [bed, peak]")
args = parser.parse_args() args = parser.parse_args()
mdb = chipathlon.db.MongoDB(args.host, args.username, args.password)
if args.type() == "bed":
mdb.save_bed(args.f, args.c, args.e, {})
elif args.type() == "peak":
mdb.save_peak(args.f, args.c, args.e, {})
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