Harmonise CLI argument names

src/talos/CPG/MakePhenopackets.py

@@ -181,9 +181,9 @@ def main(output: str, dataset: str, seq_type: str, tech: str = 'short-read', hpo
 
 def cli_main():
     parser = ArgumentParser(description='Generate a PED file for Talos')
-    parser.add_argument('dataset', help='The dataset to query for')
-    parser.add_argument('output', help='The output file')
-    parser.add_argument('type', help='Sequencing type (exome or genome)')
+    parser.add_argument('--dataset', help='The dataset to query for')
+    parser.add_argument('--output', help='The output file')
+    parser.add_argument('--type', help='Sequencing type (exome or genome)')
     parser.add_argument('--hpo', help='HPO ontology file')
     parser.add_argument('--tech', help='Sequencing technology', default='short-read')
     args = parser.parse_args()

src/talos/CPG/convert_ePED_to_phenopackets.py

@@ -17,8 +17,8 @@
 
 def cli_main():
     parser = ArgumentParser()
-    parser.add_argument('ped_file', help='path to the extended PED file')
-    parser.add_argument('output', help='stem path to write phenopacket and new PED file')
+    parser.add_argument('--input', help='path to the extended PED file')
+    parser.add_argument('--output', help='stem path to write phenopacket and new PED file')
     args = parser.parse_args()
     main(args.ped_file, args.output)
 

src/talos/CreateTalosHTML.py

@@ -32,13 +32,13 @@
 def cli_main():
     get_logger(__file__).info('Running HTML builder')
     parser = ArgumentParser()
-    parser.add_argument('--results', help='Path to analysis results', required=True)
+    parser.add_argument('--input', help='Path to analysis results', required=True)
     parser.add_argument('--panelapp', help='PanelApp data', required=True)
     parser.add_argument('--output', help='Final HTML filename', required=True)
     parser.add_argument('--latest', help='Optional second report, latest variants only')
     parser.add_argument('--split_samples', help='divides samples into sub-reports', type=int)
     args = parser.parse_args()
-    main(args.results, args.panelapp, args.output, args.latest, args.split_samples)
+    main(args.input, args.panelapp, args.output, args.latest, args.split_samples)
 
 
 def main(results: str, panelapp: str, output: str, latest: str | None = None, split_samples: int | None = None):

src/talos/FindGeneSymbolMap.py

@@ -51,7 +51,7 @@ async def match_symbol_to_ensg(gene_symbol: str, session: ClientSession) -> tupl
 def cli_main():
     parser = ArgumentParser()
     parser.add_argument('--panelapp', help='Path to the PanelApp results file', required=True)
-    parser.add_argument('--out_path', help='where to write the output (.json)', required=True)
+    parser.add_argument('--output', help='where to write the output (.json)', required=True)
     args = parser.parse_args()
 
     main(args.panelapp, out_path=args.out_path)

src/talos/GeneratePanelData.py

@@ -185,11 +185,11 @@ def match_participants_to_panels(participant_hpos: PhenotypeMatchedPanels, hpo_p
 def cli_main():
     get_logger(__file__).info('Starting HPO~Panel matching')
     parser = ArgumentParser()
-    parser.add_argument('cohort_file', help='GA4GH Cohort/PhenoPacket File')
-    parser.add_argument('output', help='Path to write PhenotypeMatchedPanels to (JSON)')
+    parser.add_argument('--input', help='GA4GH Cohort/PhenoPacket File')
+    parser.add_argument('--output', help='Path to write PhenotypeMatchedPanels to (JSON)')
     parser.add_argument('--hpo', help='Local copy of HPO obo file', required=True)
     args = parser.parse_args()
-    main(ga4gh_cohort_file=args.cohort_file, panel_out=args.output, hpo_file=args.hpo)
+    main(ga4gh_cohort_file=args.input, panel_out=args.output, hpo_file=args.hpo)
 
 
 def main(ga4gh_cohort_file: str, panel_out: str, hpo_file: str):

src/talos/HPOFlagging.py

@@ -223,19 +223,19 @@ def filter_and_write_out(annotated_results: ResultData, out_path: str):
 
 def cli_main():
     parser = ArgumentParser(description='')
-    parser.add_argument('--results', help='The Result data in JSON form')
+    parser.add_argument('--input', help='The Result data in JSON form')
     parser.add_argument('--gene_map', help='A map of gene symbol to ENSG for all genes in this analysis')
     parser.add_argument('--gen2phen', help='path to the genotype-phenotype file')
     parser.add_argument('--phenio', help='A phenio DB file')
-    parser.add_argument('--out', help='Annotated full output')
+    parser.add_argument('--output', help='Annotated full output')
     parser.add_argument('--phenout', help='Annotated phenotype-only output')
     args = parser.parse_args()
     main(
-        result_file=args.results,
+        result_file=args.input,
         gene_map=args.gene_map,
         gen2phen=args.gen2phen,
         phenio=args.phenio,
-        out_path=args.out,
+        out_path=args.output,
         phenout=args.phenout,
     )
 

src/talos/MatchGenesToPhenotypes.py

@@ -136,11 +136,11 @@ def cli_main():
     parser = ArgumentParser()
     parser.add_argument('--g2p', help='path to the genotype-phenotype file', required=True)
     parser.add_argument('--gs2id', help='path to JSON with gene symbol to Ensembl gene ID', required=True)
-    parser.add_argument('--panels', help='path to the participant-HPO-panels file', required=True)
+    parser.add_argument('--input', help='path to GeneratePanelData output', required=True)
     parser.add_argument('--phenio', help='path to the phenio db file', required=True)
     parser.add_argument('--output', help='where to write the output (.json)', required=True)
     args = parser.parse_args()
-    main(gen2phen_path=args.g2p, gs2id=args.gs2id, panels_path=args.panels, phenio_db=args.phenio, out_path=args.output)
+    main(gen2phen_path=args.g2p, gs2id=args.gs2id, panels_path=args.input, phenio_db=args.phenio, out_path=args.output)
 
 
 def main(gen2phen_path: str, gs2id: str, panels_path: str, phenio_db: str, out_path: str, min_similarity: float = 14.0):

src/talos/MinimiseOutputForSeqr.py

@@ -23,15 +23,15 @@
 
 def cli_main():
     parser = ArgumentParser()
-    parser.add_argument('input_file', help='the input file to process')
-    parser.add_argument('output_file', help='the output file to write to')
-    parser.add_argument('pheno_file', help='the output file for phenotype-matched data', default=None)
+    parser.add_argument('--input', help='the input file to process')
+    parser.add_argument('--output', help='the output file to write to')
+    parser.add_argument('--pheno', help='the output file for phenotype-matched data', default=None)
     parser.add_argument('--external_map', help='mapping of internal to external IDs for seqr', default=None)
     args = parser.parse_args()
 
-    main(input_file=args.input_file, output=args.output_file, ext_map=args.external_map)
-    if args.pheno_file:
-        main(input_file=args.input_file, output=args.pheno_file, ext_map=args.external_map, pheno_match=True)
+    main(input_file=args.input, output=args.output, ext_map=args.external_map)
+    if args.pheno:
+        main(input_file=args.input, output=args.pheno, ext_map=args.external_map, pheno_match=True)
 
 
 def main(input_file: str, output: str, ext_map: str | None = None, pheno_match: bool = False):

src/talos/QueryPanelapp.py

@@ -223,9 +223,9 @@ def get_best_moi(gene_dict: dict):
 def cli_main():
     parser = ArgumentParser()
     parser.add_argument('--panels', help='JSON of per-participant panels', default=None)
-    parser.add_argument('--out_path', required=True, help='destination for results')
+    parser.add_argument('--output', required=True, help='destination for results')
     args = parser.parse_args()
-    main(panels=args.panels, out_path=args.out_path)
+    main(panels=args.panels, out_path=args.output)
 
 
 def main(panels: str | None, out_path: str):

src/talos/RunHailFiltering.py

@@ -786,7 +786,7 @@ def cli_main():
     parser.add_argument('--mt', required=True, help='path to input MT')
     parser.add_argument('--panelapp', required=True, help='panelapp JSON')
     parser.add_argument('--pedigree', required=True, help='Cohort Pedigree')
-    parser.add_argument('--vcf_out', help='Where to write the VCF', required=True)
+    parser.add_argument('--output', help='Where to write the VCF', required=True)
     parser.add_argument('--clinvar', help='HT containing ClinvArbitration annotations', required=True)
     parser.add_argument('--pm5', help='HT containing clinvar PM5 annotations, optional', default=None)
     parser.add_argument('--checkpoint', help='Where/whether to checkpoint, String path', default=None)
@@ -795,7 +795,7 @@ def cli_main():
         mt_path=args.mt,
         panel_data=args.panelapp,
         pedigree=args.pedigree,
-        vcf_out=args.vcf_out,
+        vcf_out=args.output,
         clinvar=args.clinvar,
         pm5=args.pm5,
         checkpoint=args.checkpoint,

src/talos/RunHailFilteringSV.py

@@ -132,9 +132,9 @@ def cli_main():
     parser.add_argument('--mt', required=True, help='path to input MT')
     parser.add_argument('--panelapp', type=str, required=True, help='panelapp JSON')
     parser.add_argument('--pedigree', type=str, required=True, help='Cohort Pedigree')
-    parser.add_argument('--vcf_out', help='Where to write the VCF', required=True)
+    parser.add_argument('--output', help='Where to write the VCF', required=True)
     args = parser.parse_args()
-    main(mt_path=args.mt, panelapp_path=args.panelapp, pedigree=args.pedigree, vcf_out=args.vcf_out)
+    main(mt_path=args.mt, panelapp_path=args.panelapp, pedigree=args.pedigree, vcf_out=args.output)
 
 
 def main(mt_path: str, panelapp_path: str, pedigree: str, vcf_out: str):

src/talos/ValidateMOI.py

@@ -393,15 +393,15 @@ def cli_main():
     parser = ArgumentParser(description='Startup commands for the MOI testing phase of Talos')
     parser.add_argument('--labelled_vcf', help='Category-labelled VCF')
     parser.add_argument('--labelled_sv', help='Category-labelled SV VCF', default=[], nargs='+')
-    parser.add_argument('--out_json', help='Prefix to write JSON results to', required=True)
+    parser.add_argument('--output', help='Prefix to write JSON results to', required=True)
     parser.add_argument('--panelapp', help='Path to JSON file of PanelApp data', required=True)
     parser.add_argument('--pedigree', help='Path to joint-call PED file', required=True)
     parser.add_argument('--participant_panels', help='panels per participant', default=None)
     args = parser.parse_args()
 
     main(
         labelled_vcf=args.labelled_vcf,
-        out_json=args.out_json,
+        out_json=args.output,
         panelapp=args.panelapp,
         pedigree=args.pedigree,
         labelled_sv=args.labelled_sv,

src/talos/VcfToMt.py

@@ -350,14 +350,14 @@ def cli_main():
     """
 
     parser = ArgumentParser(description='Takes a VEP annotated VCF and makes it a MT')
-    parser.add_argument('vcf', help='Path to the annotated VCF')
-    parser.add_argument('output', help='output MatrixTable path')
+    parser.add_argument('--input', help='Path to the annotated VCF')
+    parser.add_argument('--output', help='output MatrixTable path')
     parser.add_argument('--am', help='Hail Table containing AlphaMissense annotations', default=None)
     args, unknown = parser.parse_known_args()
     if unknown:
         raise ValueError(f'Whats the deal with {unknown}?')
 
-    main(vcf_path=args.vcf, output_path=args.output, alpha_m=args.am)
+    main(vcf_path=args.input, output_path=args.output, alpha_m=args.am)
 
 
 def main(vcf_path: str, output_path: str, alpha_m: str | None = None):