Merge pull request #53 from clinical-genomics-uppsala/mosdepth

feat: mosdepth
clinical-genomics-uppsala · Dec 5, 2023 · 4ce2b2d · 4ce2b2d
2 parents 4072984 + a9e5873
commit 4ce2b2d
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Showing 2 changed files with 20 additions and 3 deletions.
diff --git a/config/multiqc_dna_config.yaml b/config/multiqc_dna_config.yaml
@@ -89,6 +89,17 @@ table_columns_visible:
     reads_MQ0_percent: False
     raw_total_sequences: True
 
+# mosdepth custom thresholds
+mosdepth_config:
+  general_stats_coverage:
+    - 1
+    - 5
+    - 10
+    - 15
+    - 20
+    - 30
+    - 50
+
 # Patriks plug in, addera egna columner till general stats
 multiqc_cgs:
   Picard:
@@ -135,9 +146,10 @@ table_columns_placement:
     1_x_pc: 666
     5_x_pc: 666
     10_x_pc: 602
-    20_x_pc: 603
-    30_x_pc: 604
-    50_x_pc: 605
+    15_x_pc: 603
+    20_x_pc: 604
+    30_x_pc: 605
+    50_x_pc: 606
   Samtools:
     raw_total_sequences: 500
     reads_mapped: 501

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -497,8 +497,13 @@ use rule mosdepth from qc as qc_mosdepth with:
         bed=temp("qc/mosdepth/{sample}_{type,T|N}.regions.bed.gz"),
         csi=temp("qc/mosdepth/{sample}_{type,T|N}.regions.bed.gz.csi"),
         glob=temp("qc/mosdepth/{sample}_{type,T|N}.mosdepth.global.dist.txt"),
+        thresholds=temp("qc/mosdepth/{sample}_{type,T|N}.thresholds.bed.gz"),
         region=temp("qc/mosdepth/{sample}_{type,T|N}.mosdepth.region.dist.txt"),
         summary=temp("qc/mosdepth/{sample}_{type,T|N}.mosdepth.summary.txt"),
+    params:
+        by=config.get("mosdepth", {}).get("by", ""),
+        extra=config.get("mosdepth", {}).get("extra", ""),
+        thresholds=config.get("mosdepth", {}).get("thresholds", ""),
 
 
 if aligner == "bwa_gpu":