Merge pull request #103 from eastgenomics/DI-293_generate_bed_prefix

add output_file_prefix string input to generate_bed stages (#103)
eastgenomics · May 17, 2023 · 1e21343 · 1e21343
2 parents 9ee9ba5 + b9e036a
commit 1e21343
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/cnvreports.py b/cnvreports.py
@@ -267,7 +267,9 @@ def run_cnvreports(
  "{}.clinical_indication".format(assay_config.cnv_generate_workbook_stage_id),
  "{}.panel".format(assay_config.cnv_generate_bed_vep_stage_id),
  "{}.panel".format(assay_config.cnv_generate_bed_excluded_stage_id),
- "{}.panel".format(assay_config.cnv_generate_workbook_stage_id)
+ "{}.panel".format(assay_config.cnv_generate_workbook_stage_id),
+ "{}.output_file_prefix".format(assay_config.cnv_generate_bed_vep_stage_id),
+ "{}.output_file_prefix".format(assay_config.cnv_generate_bed_excluded_stage_id)
  ])
  headers.append(tuple(new_headers))
 
@@ -283,7 +285,8 @@ def run_cnvreports(
  # file properly
  CIs = ";".join(CI_list)
  panels = ";".join(panel_list)
- line.extend([CIs, CIs, CIs, panels])
+ test_codes = "&&".join([CI.split("_")[0] for CI in CI_list])
+ line.extend([CIs, CIs, CIs, panels, test_codes, test_codes])
  values.append(line)
 
  job_report_dict["successful"] = len(rpt_values)

diff --git a/reports.py b/reports.py
@@ -267,7 +267,9 @@ def run_reports(
  "{}.clinical_indication".format(assay_config.generate_workbook_stage_id),
  "{}.panel".format(assay_config.generate_bed_vep_stage_id),
  "{}.panel".format(assay_config.generate_bed_athena_stage_id),
- "{}.panel".format(assay_config.generate_workbook_stage_id)
+ "{}.panel".format(assay_config.generate_workbook_stage_id),
+ "{}.output_file_prefix".format(assay_config.generate_bed_vep_stage_id),
+ "{}.output_file_prefix".format(assay_config.generate_bed_athena_stage_id)
  ])
  headers.append(tuple(new_headers))
 
@@ -283,7 +285,8 @@ def run_reports(
  # file properly
  CIs = ";".join(CI_list)
  panels = ";".join(panel_list)
- line.extend([CIs, CIs, CIs, panels])
+ test_codes = "&&".join([CI.split("_")[0] for CI in CI_list])
+ line.extend([CIs, CIs, CIs, panels, test_codes, test_codes])
  values.append(line)
 
  job_report_dict["successful"] = len(rpt_values)