diff --git a/proteosafe/msql-network-query-nf/Makefile b/proteosafe/msql-network-query-nf/Makefile
new file mode 100644
index 0000000..13aeeec
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/Makefile
@@ -0,0 +1,7 @@
+-include ../Makefile.credentials
+include ../Makefile.deploytemplate
+
+WORKFLOW_NAME=msql-nf
+TOOL_FOLDER_NAME=msql-nf
+WORKFLOW_VERSION=release_30
+WORKFLOW_DESCRIPTION="MassQL Query Workflow - Documentation Link. Currently Supports v1.0 of MassQL"
\ No newline at end of file
diff --git a/proteosafe/msql-network-query-nf/msql-nf/binding.xml b/proteosafe/msql-network-query-nf/msql-nf/binding.xml
new file mode 100644
index 0000000..373edf7
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/msql-nf/binding.xml
@@ -0,0 +1,40 @@
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diff --git a/proteosafe/msql-network-query-nf/msql-nf/flow.xml b/proteosafe/msql-network-query-nf/msql-nf/flow.xml
new file mode 100644
index 0000000..a53b303
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/msql-nf/flow.xml
@@ -0,0 +1,28 @@
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diff --git a/proteosafe/msql-network-query-nf/msql-nf/input.xml b/proteosafe/msql-network-query-nf/msql-nf/input.xml
new file mode 100644
index 0000000..74c4ec9
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/msql-nf/input.xml
@@ -0,0 +1,138 @@
+
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+ MSQL-NF
+ MSQL-NF
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diff --git a/proteosafe/msql-network-query-nf/msql-nf/result.xml b/proteosafe/msql-network-query-nf/msql-nf/result.xml
new file mode 100644
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--- /dev/null
+++ b/proteosafe/msql-network-query-nf/msql-nf/result.xml
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diff --git a/proteosafe/msql-network-query-nf/msql-nf/tool.xml b/proteosafe/msql-network-query-nf/msql-nf/tool.xml
new file mode 100644
index 0000000..1a94c3e
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/msql-nf/tool.xml
@@ -0,0 +1,73 @@
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diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/bin b/proteosafe/msql-network-query-nf/tools/msql-nf/bin
new file mode 120000
index 0000000..bfd3c00
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/bin
@@ -0,0 +1 @@
+../../../../workflow/bin/
\ No newline at end of file
diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/cluster.config b/proteosafe/msql-network-query-nf/tools/msql-nf/cluster.config
new file mode 120000
index 0000000..1ac268f
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/cluster.config
@@ -0,0 +1 @@
+../../../msql-repo-full-nf/tools/msql-repo-full-nf/cluster.config
\ No newline at end of file
diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/demangle_collection.py b/proteosafe/msql-network-query-nf/tools/msql-nf/demangle_collection.py
new file mode 100644
index 0000000..b577c1d
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/demangle_collection.py
@@ -0,0 +1,94 @@
+from pathlib import Path
+import xmltodict
+import argparse
+from csv import DictReader
+from collections import defaultdict
+import sys
+import shutil
+
+def arguments():
+ parser = argparse.ArgumentParser(description='Demangle collection as aliases to folder')
+ parser.add_argument('-p','--params', type = Path, help='ProteoSAFe params.xml')
+ parser.add_argument('-i','--input_folder', type = Path, help='Input folder path')
+ parser.add_argument('-m','--input_mangled_prefix', type = str, help='Mangled prefix for input')
+ parser.add_argument('-o','--output_folder', type = Path, help='Output folder path')
+ parser.add_argument('-l','--output_list', type = Path, help='Output list of paths')
+ parser.add_argument('-r','--reverse', dest='reverse', action='store_true', help='Flag to demangle file collection')
+ parser.add_argument('-s','--preserve_suffix', dest='preserve_suffix', action='store_true', help='Flag to save suffix from demangled file collection')
+ parser.add_argument('-c','--copy', dest='copy', action='store_true', help='Flag to copy files into destination instead of symlink them')
+ return parser.parse_args()
+
+def read_params(input_file, mangled_prefix):
+ return get_mangled_file_mapping(parse_xml_file(input_file),mangled_prefix)
+
+def get_mangled_file_mapping(params, mangled_prefix):
+ all_mappings = params["upload_file_mapping"]
+ mangled_mapping = {}
+ demangled_mapping = {}
+ for mapping in all_mappings:
+ splits = mapping.split("|")
+ mangled_name = splits[0]
+ original_name = splits[1]
+ if mangled_prefix in mangled_name:
+ mangled_mapping[mangled_name] = Path(original_name)
+ demangled_mapping[original_name] = Path(mangled_name)
+ return mangled_mapping, demangled_mapping
+
+def parse_xml_file(input_file):
+ with open(input_file) as f:
+ key_value_pairs = defaultdict(list)
+ xml_obj = xmltodict.parse(f.read())
+
+ #print(json.dumps(xml_obj["parameters"]))
+ for parameter in xml_obj["parameters"]["parameter"]:
+ name = parameter["@name"]
+ value = parameter["#text"]
+ key_value_pairs[name].append(value)
+
+ return key_value_pairs
+
+def main():
+
+ # don't fail on error, since it is likely to be run without inputs
+ args = arguments()
+
+ if not (args.input_folder and args.output_folder and args.params and args.input_mangled_prefix):
+ print("Input folder, output folder, params, and collection prefix are required.")
+ sys.exit(0)
+ mangled_mapping, demangled_mapping = read_params(args.params, args.input_mangled_prefix)
+ output_list = None
+
+ if args.output_list:
+ output_list = open(args.output_list, 'w')
+
+ for input_file in args.input_folder.rglob('*'):
+
+ if input_file.is_file():
+
+ input_path = args.input_folder.joinpath('/'.join(input_file.parts[1:])).absolute()
+
+ if args.reverse:
+ if args.preserve_suffix:
+ suffix = input_file.suffix
+ input_file_str_no_suffix = '/'.join(input_file.with_suffix('').parts[1:])
+ output_file = demangled_mapping.get(input_file_str_no_suffix).with_suffix(suffix)
+ else:
+ output_file = demangled_mapping.get('/'.join(input_file.parts[1:]))
+ else:
+ output_file = mangled_mapping.get(input_file.name)
+
+ output_path = args.output_folder.joinpath(output_file)
+ output_path.parent.mkdir(parents=True, exist_ok=True)
+ if not args.copy:
+ output_path.symlink_to(input_path)
+ else:
+ shutil.copyfile(input_path, output_path)
+
+ if output_list:
+ output_list.write('{}\n'.format(output_path))
+
+ if output_list:
+ output_list.close()
+
+if __name__ == "__main__":
+ main()
\ No newline at end of file
diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/ming_fileio_library.py b/proteosafe/msql-network-query-nf/tools/msql-nf/ming_fileio_library.py
new file mode 120000
index 0000000..a983167
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/ming_fileio_library.py
@@ -0,0 +1 @@
+../../../msql/tools/msql/ming_fileio_library.py
\ No newline at end of file
diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/ming_proteosafe_library.py b/proteosafe/msql-network-query-nf/tools/msql-nf/ming_proteosafe_library.py
new file mode 120000
index 0000000..43f41fb
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/ming_proteosafe_library.py
@@ -0,0 +1 @@
+../../../msql/tools/msql/ming_proteosafe_library.py
\ No newline at end of file
diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/nextflow_wrapper.py b/proteosafe/msql-network-query-nf/tools/msql-nf/nextflow_wrapper.py
new file mode 100644
index 0000000..3a8f98a
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/nextflow_wrapper.py
@@ -0,0 +1,137 @@
+import json
+import os
+import argparse
+import glob
+import sys
+import shutil
+import pandas as pd
+import ming_proteosafe_library
+import pathlib
+
+
+def main():
+ parser = argparse.ArgumentParser(description="Proteosafe Wrapper for Nextflow")
+ parser.add_argument('workflow_params', help='workflow_params, from proteosafe')
+ parser.add_argument('nextflow_script', help='nextflow_script to actually run')
+ parser.add_argument('conda_activate', help='conda_activate, this is the path to the activate command in the main conda installation')
+ parser.add_argument('nextflow_conda_environment', help='nextflow_conda_environment, this likely should be wherever all your dependencies and nextflow are installed, e.g. nextflow or msql2')
+ parser.add_argument('--parametermapping', action='append', help='mapping of current workflow parameters to new parameters in the format: :')
+ parser.add_argument('--newparameters', action='append', help='parameter key: :')
+
+ parser.add_argument('--metricoutput', default=None, help='output folder for metrics')
+
+ # Settings if we want to monitor nextflow progress in ProteoSAFe
+ parser.add_argument('--updateproteosafefronteendstatus', default='NO', help='Enables outputting data to front end task directories to allow for current status, options YES and NO')
+
+ # These settings are for the cluster run
+ parser.add_argument('--runcluster', default='NO', help='Tries to run this on the cluster, values are NO and YES')
+ parser.add_argument('--clusterconfig', default=None, help='Path to configuration file')
+ parser.add_argument('--user', default=None, help='username running the task')
+ parser.add_argument('--clusterpythonruntime', default=None, help='cluster python runtime')
+ parser.add_argument('--clusterworkprefix', default=None, help='clusterworkprefix')
+ parser.add_argument('--task', default=None, help='cluster python runtime')
+
+ args = parser.parse_args()
+
+ # Listing our system
+ os.system("hostname")
+ os.system("whoami")
+ os.system("pwd")
+ os.system("ls -l -h")
+
+ output_stdout_file = os.path.abspath(os.path.join(args.metricoutput, "stdout.log"))
+ workflow_task_directory = "."
+ original_directory = os.getcwd()
+
+ output_trace_filename = "trace.txt"
+
+ if args.updateproteosafefronteendstatus == "YES":
+ output_trace_folder = os.path.join("/data/ccms-data/tasks/", args.user, args.task, "nextflow")
+ pathlib.Path(output_trace_folder).mkdir(parents=True, exist_ok=True)
+ output_trace_filename = os.path.join(output_trace_folder, "trace.txt")
+
+ output_stdout_file = os.path.join(output_trace_folder, "stdout.log")
+
+ if args.runcluster == "YES" and args.user in ["mwang87"]:
+ # Staging all files on gscratch because they might not be seen if we schedule outputs from local scratch disk
+ workflow_task_directory = os.path.join("/gscratch/nextflow_staging", args.task)
+ pathlib.Path(workflow_task_directory).mkdir(parents=True, exist_ok=True)
+
+ pbs_cluster_work_dir = os.path.join(args.clusterworkprefix, args.task, "work")
+
+ cmd = "source {} {} && \
+ export NXF_OPTS='-Xms35G -Xmx35G' && \
+ cd {} && nextflow run {} -c {} \
+ -work-dir {} \
+ -resume \
+ --PYTHONRUNTIME={} \
+ -with-trace {} \
+ -with-dag dag.html \
+ -with-report report.html \
+ -with-timeline timeline.html > {} 2>&1".format(args.conda_activate, args.nextflow_conda_environment,
+ workflow_task_directory,
+ args.nextflow_script, args.clusterconfig, pbs_cluster_work_dir, args.clusterpythonruntime,
+ output_trace_filename,
+ output_stdout_file)
+ else:
+ cmd = "source {} {} && nextflow run {} \
+ -with-trace {} \
+ -with-dag dag.html \
+ -with-report report.html \
+ -with-timeline timeline.html > {} 2>&1".format(args.conda_activate, args.nextflow_conda_environment,
+ args.nextflow_script,
+ output_trace_filename,
+ output_stdout_file)
+ for parameter in args.newparameters:
+ print(parameter)
+ cmd += ' --{} "{}"'.format(parameter.split(":")[0], parameter.split(":")[1].replace("\n", ""))
+
+ params_obj = ming_proteosafe_library.parse_xml_file(open(args.workflow_params))
+ for parameter in args.parametermapping:
+ print(parameter)
+ new_param = parameter.split(":")[1]
+ old_param = parameter.split(":")[0]
+
+ cmd += ' --{} "{}"'.format(new_param, params_obj[old_param][0].replace("\n", ""))
+
+ # Saving the script
+ output_script = os.path.abspath(os.path.join(args.metricoutput, "run_nf.sh"))
+ with open(output_script, "w") as f:
+ f.write(cmd)
+
+ print(cmd)
+ return_val = os.system(cmd)
+ if return_val != 0:
+ print("Error in Nextflow")
+
+ # Copying back results
+ if workflow_task_directory != ".":
+ try:
+ cmd = "rsync -avp {}/ {}".format(workflow_task_directory, original_directory)
+ print(cmd)
+ os.system(cmd)
+ except:
+ pass
+
+ # Copying the metric output to output folder
+ if args.metricoutput is not None:
+ try:
+ shutil.copyfile(output_trace_filename, os.path.join(args.metricoutput, "trace.txt"))
+ except:
+ pass
+
+ try:
+ shutil.copyfile(output_stdout_file, os.path.join(args.metricoutput, "stdout.log"))
+ except:
+ pass
+
+ try:
+ shutil.copyfile("report.html", os.path.join(args.metricoutput, "report.html"))
+ shutil.copyfile("timeline.html", os.path.join(args.metricoutput, "timeline.html"))
+ shutil.copyfile("dag.html", os.path.join(args.metricoutput, "dag.html"))
+ except:
+ pass
+
+
+if __name__ == "__main__":
+ main()
diff --git a/proteosafe/msql-network-query-nf/tools/msql-nf/workflow.nf b/proteosafe/msql-network-query-nf/tools/msql-nf/workflow.nf
new file mode 120000
index 0000000..75ff0e3
--- /dev/null
+++ b/proteosafe/msql-network-query-nf/tools/msql-nf/workflow.nf
@@ -0,0 +1 @@
+../../../../workflow/workflow.nf
\ No newline at end of file