Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Klinische Genetica
capture-lumc
hutspot
Commits
aebad7df
Commit
aebad7df
authored
Jul 28, 2020
by
van den Berg
Browse files
Add memory settings for hs_metrics and multiple_metrics
parent
e2c4274e
Changes
2
Hide whitespace changes
Inline
Side-by-side
Snakefile
View file @
aebad7df
...
...
@@ -464,7 +464,7 @@ rule multiple_metrics:
alignment = "{sample}/bams/{sample}.alignment_summary_metrics",
insertMetrics = "{sample}/bams/{sample}.insert_size_metrics"
container: containers["picard"]
shell: "picard CollectMultipleMetrics "
shell: "picard
-Xmx8G -XX:CompressedClassSpaceSize=256m
CollectMultipleMetrics "
"I={input.bam} O={params.prefix} "
"R={input.ref} "
"PROGRAM=CollectAlignmentSummaryMetrics "
...
...
@@ -501,7 +501,7 @@ rule hs_metrics:
baits = rules.bed_to_interval.output.baits_interval,
output: "{sample}/bams/{sample}.hs_metrics.txt"
container: containers["picard"]
shell: "picard CollectHsMetrics "
shell: "picard
-Xmx8G -XX:CompressedClassSpaceSize=256m
CollectHsMetrics "
"I={input.bam} O={output} "
"R={input.ref} "
"BAIT_INTERVALS={input.baits} "
...
...
cluster/sge_cluster.yml
View file @
aebad7df
...
...
@@ -9,8 +9,14 @@ align:
bed_to_interval
:
threads
:
1
vmem
:
16G
hs_metrics
:
threads
:
1
vmem
:
20G
markdup
:
vmem
:
20G
multiple_metrics
:
threads
:
1
vmem
:
20G
baserecal
:
threads
:
8
vmem
:
6G
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment