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fix: give melt more memory (#372)
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holtgrewe authored Feb 9, 2023
1 parent 05f7988 commit 33785b2
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Showing 6 changed files with 6 additions and 6 deletions.
2 changes: 1 addition & 1 deletion snappy_pipeline/workflows/common/melt.py
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Expand Up @@ -43,7 +43,7 @@ class MeltStepPart(
_resource_usage = ResourceUsage(
threads=1,
time="1-00:00:00",
memory="6G",
memory="12G",
)
resource_usage_dict = {
"preprocess": _resource_usage,
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/melt/genotype/wrapper.py
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Expand Up @@ -16,7 +16,7 @@
ME_REFS={melt_config[me_refs_path]}
ME_INFIX={melt_config[me_refs_infix]}
java -Xmx6G -jar $JAR \
java -Xmx8G -jar $JAR \
Genotype \
-h {snakemake.config[static_data_config][reference][path]} \
-bamfile {snakemake.input.bam} \
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/melt/group_analysis/wrapper.py
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Expand Up @@ -16,7 +16,7 @@
ME_REFS={melt_config[me_refs_path]}
ME_INFIX={melt_config[me_refs_infix]}
java -jar -Xmx6G -jar $JAR \
java -jar -Xmx8G -jar $JAR \
GroupAnalysis \
-h {snakemake.config[static_data_config][reference][path]} \
-t $ME_REFS/$ME_INFIX/{snakemake.wildcards.me_type}_MELT.zip \
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py
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Expand Up @@ -17,7 +17,7 @@
ME_REFS={melt_config[me_refs_path]}
ME_INFIX={melt_config[me_refs_infix]}
java -Xmx6G -jar $JAR \
java -Xmx8G -jar $JAR \
IndivAnalysis \
-b hs37d5/NC_007605 \
{melt_arg_exome} \
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/melt/make_vcf/wrapper.py
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Expand Up @@ -22,7 +22,7 @@
> {snakemake.output.list_txt}
# TODO: allowing 100% no-call wise?
java -Xmx6G -jar $JAR \
java -Xmx8G -jar $JAR \
MakeVCF \
-genotypingdir $genotype_dir \
-h {snakemake.config[static_data_config][reference][path]} \
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2 changes: 1 addition & 1 deletion snappy_wrappers/wrappers/melt/preprocess/wrapper.py
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Expand Up @@ -17,7 +17,7 @@
JAR={melt_config[jar_file]}
java -Xmx4G -jar $JAR \
java -Xmx8G -jar $JAR \
Preprocess \
-bamfile {snakemake.output.orig_bam} \
-h {snakemake.config[static_data_config][reference][path]}
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