fix: Increase sambamba run time (#1001)

Clinical-Genomics · Sep 27, 2022 · f357440 · f357440
1 parent 48022a4
commit f357440
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Showing 3 changed files with 13 additions and 3 deletions.
diff --git a/BALSAMIC/config/cluster.json b/BALSAMIC/config/cluster.json
@@ -85,7 +85,7 @@
  "n": 4
  },
  "sambamba_exon_depth": {
- "time": "02:30:00",
+ "time": "04:00:00",
  "n": 8
  },
  "sambamba_panel_depth": {

diff --git a/BALSAMIC/snakemake_rules/quality_control/sambamba_depth.rule b/BALSAMIC/snakemake_rules/quality_control/sambamba_depth.rule
@@ -32,6 +32,7 @@ sambamba depth region \
 --regions {input.bed} \
 --min-base-quality={params.base_qual} \
 --filter {params.filter_string} \
+--nthreads {threads} \
 `echo $covStr` {input.bam} > {output}; 
  """
 
@@ -67,5 +68,6 @@ sambamba depth region \
 --filter {params.filter_string} \
 --cov-threshold {params.cov_1} --cov-threshold {params.cov_2} \
 --cov-threshold {params.cov_3} --cov-threshold {params.cov_4} \
---cov-threshold {params.cov_5} {input.bam} > {output};
+--cov-threshold {params.cov_5} \
+--nthreads {threads} {input.bam} > {output};
  """
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,14 @@
-[10.0.3]
+[10.0.4]
+---------
+Fixed:
+^^^^^^
 
+* Increase sambamba_exon_depth rule run time https://github.com/Clinical-Genomics/BALSAMIC/pull/1001
+
+[10.0.3]
+---------
 Fixed:
+^^^^^^
 
 * Input VCF files for cnvkit rules, cnvkit command and container https://github.com/Clinical-Genomics/BALSAMIC/pull/995