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Merge pull request #166 from sangeetashukla/deseq_cavatica_publishing
Enable using module to publish cavatica app
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88 changes: 88 additions & 0 deletions
88
analyses/tumor-normal-differential-expression/workflows/cavatica_app_pub.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| import argparse | ||
| from ruamel import yaml | ||
| from ruamel.yaml.scalarstring import PreservedScalarString as pss | ||
| import sys | ||
| import pdb | ||
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| parser = argparse.ArgumentParser() | ||
| parser.add_argument('-i', '--input-cwl', action='store', dest='cwl', help='Input cwl file',required=True) | ||
| parser.add_argument('-r', '--readme', action='store', dest='readme', help='Readme file to insert into workflow/tool doc, if applicable', required=False) | ||
| parser.add_argument('-n', '--id-name', action='store', dest='id_name', help='Short app ID link name to use, i.e. kfdrc-align-wf', required=False) | ||
| parser.add_argument('-l', '--label', action='store', dest='label', help='User-friendly label to add to tool/workflow cwl, if needed', required=False) | ||
| parser.add_argument('-t', '--tags', action='store', dest='tags', help='Seven bridges tags file, as csv string, ex RNASEQ,FUSION', required=False) | ||
| parser.add_argument('-f', '--files', action='store', dest='files', help='Cavatica-style tsv manifest with file ID, file name, associated cwl input key, and, optionally, secondaryFile names and IDs', required=False) | ||
| parser.add_argument('-p', '--publisher', action='store', dest='pub', help='Publisher name', required=False, default="KFDRC") | ||
| args = parser.parse_args() | ||
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| def update_file_paths(manifest, yaml_obj): | ||
| mf = open(manifest) | ||
| head = next(mf) # fields: fid,name,key,sfids,snames | ||
| # see if more than one file exists for input keys - will determine if values is to be File or File[] | ||
| in_dict = {} | ||
| for entry in mf: | ||
| info = [None] * 5 | ||
| data = entry.rstrip('\n').split('\t') | ||
| info[:len(data)] = data | ||
| fid,name,key,sfids,snames = info | ||
| if sfids in [None,"None"]: | ||
| dat = {"class":"File","path":fid,"name":name} | ||
| else: | ||
| assert len(sfids.split(',')) == len(snames.split(',')), "Lengths of secondaryFile IDs and names MUST BE equal" | ||
| sfidsList = sfids.split(',') | ||
| snamesList = snames.split(',') | ||
| sfileList = [] | ||
| for i in range(len(sfidsList)): | ||
| sfileList.append({"class":"File","path":sfidsList[i],"name":snamesList[i]}) | ||
| dat = {"class":"File","path":fid,"name":name,"secondaryFiles":sfileList} | ||
| if key not in in_dict: | ||
| in_dict[key] = [] | ||
| in_dict[key].append(dat) | ||
| for key in in_dict: | ||
| if len(in_dict[key]) == 1: | ||
| yaml_obj['inputs'][key]["sbg:suggestedValue"] = in_dict[key][0] | ||
| else: | ||
| yaml_obj['inputs'][key]["sbg:suggestedValue"] = in_dict[key] | ||
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| # round tripper preservers order and formatting of keys and values | ||
| data = yaml.load(open(args.cwl), yaml.RoundTripLoader, preserve_quotes=True) | ||
| if args.files: | ||
| update_file_paths(args.files, data) | ||
| # check for license, pub | ||
| if 'sbg:license' not in data: | ||
| data['sbg:license'] = "Apache License 2.0" | ||
| if 'sbg:publisher' not in data: | ||
| data['sbg:publisher'] = args.pub | ||
| if args.tags: | ||
| data['sbg:categories'] = [] | ||
| for tag in sorted(args.tags.split(',')): | ||
| data['sbg:categories'].append(tag) | ||
| key_list = list(data.keys()) | ||
| if args.label: | ||
| data.insert(key_list.index('id')+1, 'label', args.label) | ||
| data['label'] = args.label | ||
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| if args.readme: | ||
| rm = open(args.readme) | ||
| rm_str = rm.read() | ||
| rm.close() | ||
| # code from should improve readme appearance | ||
| pss_rm_str = pss(rm_str) | ||
| key_list = list(data.keys()) | ||
| if 'doc' not in data: | ||
| try: | ||
| data.insert(key_list.index('label')+1, 'doc', pss_rm_str) | ||
| except Exception as e: | ||
| sys.stderr.write(str(e) + "\nFailed to add doc field after label field, trying after id\n") | ||
| data.insert(key_list.index('id')+1, 'doc', pss_rm_str) | ||
| else: | ||
| data['doc'] = pss_rm_str | ||
| if args.id_name: | ||
| key_list = list(data.keys()) | ||
| if 'id' not in data: | ||
| data.insert(key_list.index('class')+1, 'id', args.id_name) | ||
| else: | ||
| data['id'] = args.id_name | ||
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| yaml.dump(data, sys.stdout, Dumper=yaml.RoundTripDumper, default_flow_style=False) |
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analyses/tumor-normal-differential-expression/workflows/cavatica_app_readme.txt
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| #Introduction | ||
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| DESeq application takes the gene expression counts data from the pediatric cancer cohorts and normal tissue from GTEx to determine the differential expression genes between all pediatric tumors and normal tissue. This data will be used in the Open Targets platform to help investigators identify potential therapeutic targets in various childhood cancers. | ||
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| #Method | ||
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| This app uses R for data manipulation and differential expression analysis using packages DESeq2, jsonlite, among others. | ||
| The data set includes cancers with at least 3 cases, and DESeq analysis was performed on every combination of tumor and normal tissue. Data files for the analysis are available in the [OpenTarget Open Access](http://https://cavatica.sbgenomics.com/u/cavatica/opentarget "OpenTarget Open Access") (now Molecular Targets) project. User can also choose to upload their files in similar format. | ||
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| #Result | ||
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| The app delivers analysis output for each cancer cohort and normal tissue pair, with the gene symbol, logfc, pval, EFO ID, MONDO ID, mean TPM values in jsonl, json, and tsv formats. | ||
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| #Contact | ||
| For additional information or questions, contact [Alvin Farrel](mailto:farrela@chop.edu) or [Sangeeta Shukla](mailto:shuklas1@chop.edu). |
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