reconnect to the overall workflow [ci skip]

TORCH-Consortium · Jun 23, 2024 · 39b28af · 39b28af
1 parent c9b516a
commit 39b28af
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Showing 2 changed files with 27 additions and 41 deletions.
diff --git a/bin/fastq_cohort_validation.py b/bin/fastq_cohort_validation.py
@@ -10,63 +10,48 @@
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Summarize the input FASTQ validation report')
 
-    parser.add_argument('joint_vcf_name', metavar='joint_vcf_name', default="joint", type=str,
-                        help='The prefix name of joint analysis used for used in the pipeline')
+    parser.add_argument('magma_samplesheet', metavar='magma_samplesheet',  type=str, help='')
+
+    parser.add_argument('merged_fastq_reports', metavar='merged_fastq_reports',  type=str, help='')
+
+    parser.add_argument('magma_analysis', metavar='magma_analysis',  type=str, help='')
 
-    args = vars(parser.parse_args())
 
-    vcf_name = args['joint_vcf_name']
+    args = vars(parser.parse_args())
 
     # ============================================
     # Parse the validation reports for exact sample names which passed/failed
     # ============================================
 
     # Load the JSON file into a dictionary
-    with open('merged_fastq_reports.json', 'r') as f:
+    with open(args['merged_fastq_reports'], 'r') as f:
         fastq_report_dict = json.load(f)
 
-    with open('samplesheet.json', 'r') as f:
-        magma_analysis_dict = json.load(f)
+    with open(args['magma_samplesheet'], 'r') as f:
+        magma_samplesheet_json = json.load(f)
 
     fastq_report_keys_list = list(fastq_report_dict.keys())
 
-    for k in magma_analysis_dict.keys():
-        magma_analysis_dict[k]["fastq_report"] = {}
 
-        if magma_analysis_dict[k]['R1'] is not None:
-            fastq_1_name = magma_analysis_dict[k]['R1'].split("/")[-1]
-            magma_analysis_dict[k]["fastqs_approved"] = True
+    for elem in magma_samplesheet_json:
+        elem["fastq_report"] = {}
+
+        if elem['R1'] is not None:
+            fastq_1_name = elem['R1'].split("/")[-1]
+            elem["fastqs_approved"] = True
             if fastq_1_name in fastq_report_keys_list:
-                magma_analysis_dict[k]["fastq_report"][fastq_1_name] = {"file": fastq_report_dict[fastq_1_name]}
+                elem["fastq_report"][fastq_1_name] = {"file": fastq_report_dict[fastq_1_name]}
             else:
-                magma_analysis_dict[k]["fastq_report"][fastq_1_name] = {"fastq_utils_check": "failed"}
-                magma_analysis_dict[k]["fastqs_approved"] = False
+                elem["fastq_report"][fastq_1_name] = {"fastq_utils_check": "failed"}
+                elem["fastqs_approved"] = False
 
-        if magma_analysis_dict[k]['R2'] is not None:
-            fastq_2_name = magma_analysis_dict[k]['R2'].split("/")[-1]
+        if elem['R2'] != "" :
+            fastq_2_name = elem['R2'].split("/")[-1]
             if fastq_2_name in fastq_report_keys_list:
-                magma_analysis_dict[k]["fastq_report"][fastq_2_name] = {"file": fastq_report_dict[fastq_2_name]}
+                elem["fastq_report"][fastq_2_name] = {"file": fastq_report_dict[fastq_2_name]}
             else:
-                magma_analysis_dict[k]["fastq_report"][fastq_2_name] = {"fastq_utils_check": "failed"}
-                magma_analysis_dict[k]["fastqs_approved"] = False
-
-    with open('magma_analysis.json', 'w') as f:
-        json.dump(magma_analysis_dict, f, indent=4, ensure_ascii= False)
-
-# ============================================
-# Parse the validation reports for exact sample names which passed/failed
-# ============================================
-
-    # Filter the dictionary for samples with fastqs_approved == True and False
-    approved_samples = {k for k, v in magma_analysis_dict.items() if v["fastqs_approved"] == True}
-    # Write approved_samples to a txt file with newline
-    with open("approved_samples.txt", "w") as f:
-        for sample in approved_samples:
-            f.write(sample + "\n")
-
-    rejected_samples = {k for k, v in magma_analysis_dict.items() if v["fastqs_approved"] == False}
-    # Write approved_samples to a txt file with newline
-    if rejected_samples:
-        with open("rejected_samples.txt", "w") as f:
-            for sample in rejected_samples:
-                f.write(sample + "\n")
+                elem["fastq_report"][fastq_2_name] = {"fastq_utils_check": "failed"}
+                elem["fastqs_approved"] = False
+
+    with open(args['magma_analysis'], 'w') as f:
+        json.dump(magma_samplesheet_json, f, indent=4, ensure_ascii= False)
diff --git a/modules/utils/.#fastq_cohort_validation.nf b/modules/utils/.#fastq_cohort_validation.nf
@@ -0,0 +1 @@
+abhi@macbookpro19.local.70572