Merge branch 'release_v18.0.0' of github.com:Clinical-Genomics/BALSAMIC into release_v18.0.0

Author: mathiasbio

BALSAMIC/assets/scripts/collect_qc_metrics.py

@@ -77,7 +77,7 @@ def collect_qc_metrics(
         )
 
 
-def get_multiqc_data_source(multiqc_data: dict, sample: str, tool: str) -> str:
+def get_multiqc_data_source(multiqc_data: dict, sampleid: str, tool: str) -> str:
     """Extracts the metrics data source associated with a specific sample and tool
 
     Args:
@@ -105,20 +105,13 @@ def get_multiqc_data_source(multiqc_data: dict, sample: str, tool: str) -> str:
                 subtool_name[1].lower() in source_tool.lower()
                 and subtool_name[2].lower() in source_subtool.lower()
             ):
-                try:
-                    return os.path.basename(
-                        multiqc_data["report_data_sources"][source_tool][
-                            source_subtool
-                        ][sample]
-                    )
-                except KeyError:
-                    # Deletes pair orientation information from the sample name (insertSize metrics)
-                    sample = sample.rsplit("_", 1)[0]
-                    return os.path.basename(
-                        multiqc_data["report_data_sources"][source_tool][
-                            source_subtool
-                        ][sample]
-                    )
+                source_dict = multiqc_data["report_data_sources"][source_tool][
+                    source_subtool
+                ]
+                metric_file = next(
+                    (v for k, v in source_dict.items() if sampleid in k), None
+                )
+                return os.path.basename(metric_file)
 
 
 def get_sex_check_metrics(sex_prediction_path: str, config: dict) -> list:
@@ -265,7 +258,7 @@ def extract(data, output_metrics, multiqc_key=None, source=None):
                             Metric(
                                 id=get_sample_id(multiqc_key),
                                 input=get_multiqc_data_source(
-                                    multiqc_data, multiqc_key, source
+                                    multiqc_data, get_sample_id(multiqc_key), source
                                 ),
                                 name=k,
                                 step=source,

BALSAMIC/constants/workflow_profile/config.yaml

@@ -126,6 +126,9 @@ set-resources:
   vardict_tumor_only:
     runtime: 280
     mem_mb: min(230000, 20000 * attempt)
+  vardict_move_svs:
+    runtime: 280
+    mem_mb: min(230000, 5000 * attempt)
   sentieon_tnscope_tga_tumor_only:
     runtime: 280
     mem_mb: min(230000, 20000 * attempt)
@@ -448,13 +451,13 @@ set-resources:
     mem_mb: min(230000, 30000 * attempt)
   sentieon_align_sort:
     runtime: 1440
-    mem_mb: min(230000, 15000 * attempt)
+    mem_mb: min(230000, 30000 * attempt)
   sentieon_realign:
     runtime: 1440
     mem_mb: min(230000, 80000 * attempt)
   sentieon_align_sort_umireads:
     runtime: 1440
-    mem_mb: min(230000, 15000 * attempt)
+    mem_mb: min(230000, 22000 * attempt)
   cap_base_quality:
     mem_mb: min(230000, 10000 * attempt)
     runtime: 300
@@ -463,12 +466,12 @@ set-resources:
     mem_mb: min(230000, 80000 * attempt)
   sentieon_dedup_consensus:
     runtime: 1440
-    mem_mb: min(230000, 20000 * attempt)
+    mem_mb: min(230000, 30000 * attempt)
   sentieon_base_calibration:
     mem_mb: min(230000, 25000 * attempt)
     runtime: 1440
   samtools_fixmate:
-    mem_mb: min(230000, 40000 * attempt)
+    mem_mb: min(230000, 50000 * attempt)
     runtime: 560
   bam_compress_tumor:
     mem_mb: min(230000, 8000 * attempt)
@@ -494,8 +497,12 @@ set-resources:
   samtools_merge_bamfiles:
     mem_mb: min(230000, 70000 * attempt)
     runtime: 800
+  create_final_vcf_namemap:
+    mem_mb: min(230000, 2000 * attempt)
+    runtime: 800
 
 set-threads:
+  create_final_vcf_namemap: 2
   post_process_tnscope_info_fields_wgs: 1
   post_process_tnscope_info_fields_tga: 1
   tnscope_sort: 1
@@ -534,6 +541,7 @@ set-threads:
   sentieon_tnscope_tga_tumor_normal: 16
   post_process_vardict: 2
   vardict_tumor_only: 16
+  vardict_move_svs: 2
   sentieon_tnscope_tga_tumor_only: 16
   bcftools_quality_filter_TNscope_umi_tumor_only: 8
   bcftools_quality_filter_TNscope_umi_tumor_normal: 8

CHANGELOG.rst

@@ -42,6 +42,7 @@ Removed:
 Fixed:
 ^^^^^^
 * Fixed varcall_py27 container for Manta https://github.com/Clinical-Genomics/BALSAMIC/pull/1567
+* qc metrics script bug https://github.com/Clinical-Genomics/BALSAMIC/pull/1615
 
 
 [17.1.0]