Add picard AlignmentSummaryMetrics

Snakefile

@@ -525,6 +525,7 @@ rule multiqc:
     output:
         html = "multiqc_report/multiqc_report.html",
         insert = "multiqc_report/multiqc_data/multiqc_picard_insertSize.json",
+        AlignmentMetrics = "multiqc_report/multiqc_data/multiqc_picard_AlignmentSummaryMetrics.json",
         HsMetrics = "multiqc_report/multiqc_data/multiqc_picard_HsMetrics.json" if "baitsfile" in config else []
     container: containers["multiqc"]
     shell: "multiqc --data-format json --force --outdir multiqc_report . "
@@ -537,11 +538,13 @@ rule merge_stats:
                       sample=config['samples']),
         mpy = config["merge_stats"],
         insertSize = rules.multiqc.output.insert,
+        AlignmentMetrics = rules.multiqc.output.AlignmentMetrics,
         HsMetrics = rules.multiqc.output.HsMetrics
     output: "stats.json"
     container: containers["vtools"]
     shell: "python {input.mpy} --collectstats {input.cols} "
            "--picard-insertSize {input.insertSize} "
+           "--picard-AlignmentMetrics {input.AlignmentMetrics} "
            "--picard-HsMetrics {input.HsMetrics} > {output}"
 
 rule stats_tsv:

src/merge_stats.py

@@ -58,6 +58,18 @@ def add_picard_HsMetrics(data, filename):
             raise RuntimeError(f"Unknown sample {sample}")
 
 
+def add_picard_AlignmentMetrics(data, filename):
+    AlignmentMetrics = parse_json(filename)
+
+    for sample in AlignmentMetrics:
+        for d in data['sample_stats']:
+            if d['sample_name'] == sample:
+                d['picard_AlignmentSummaryMetrics'] = AlignmentMetrics[sample]
+                break
+        else:
+            raise RuntimeError(f"Unknown sample {sample}")
+
+
 def main(args):
     data = dict()
     data["sample_stats"] = list()
@@ -71,6 +83,11 @@ def main(args):
 
     if args.picard_HsMetrics:
         add_picard_HsMetrics(data, args.picard_HsMetrics)
+
+    if args.picard_AlignmentMetrics:
+        add_picard_AlignmentMetrics(data,
+                args.picard_AlignmentMetrics)
+
     print(json.dumps(data))
 
 
@@ -90,5 +107,10 @@ if __name__ == "__main__":
                         nargs='?',
                         help=('Path to multiQC json summary for picard '
                         'HsMetrics'))
+    parser.add_argument('--picard-AlignmentMetrics',
+                        required=False,
+                        nargs='?',
+                        help=('Path to multiQC json summary for picard '
+                        'AlignmentSummaryMetrics'))
     args = parser.parse_args()
     main(args)

tests/test_integration_run.yml

@@ -39,6 +39,7 @@
       contains:
         - MEDIAN_INSERT_SIZE
         - WIDTH_OF_99_PERCENT
+        - picard_AlignmentSummaryMetrics
 
 - name: test-integration-small-scatter
   tags: