Commit e13cb2a1 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

changed resources

parent b8901a18
......@@ -12,8 +12,8 @@ rule estimateKmerCoverage:
#cluster execution
cpus = '1', #TODO: This could in theory be sped up significantly using a shared cache and multithreading
gpus = '0',
mem = '64G',
walltime = '00:45:00'
mem = '6G',
walltime = '00:10:00'
log:
'logs/' + config['input_folder'] + '/kmers/{kmer}/{id}/estimateKmerCoverage.log'
benchmark:
......
......@@ -82,9 +82,9 @@ rule bwa:
params:
#cluster execution
cpus = '1',
mem = '32G',
mem = '1G',
gpus = '0',
walltime = '00:30:00'
walltime = '00:10:00'
singularity:
'docker://biocontainers/bwa:v0.7.17-3-deb_cv1'
shell:
......@@ -358,7 +358,11 @@ rule calcKmerErrorRates:
output:
error = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/error_estimate.txt'
params:
k = lambda wildcards: wildcards.kmer
k = lambda wildcards: wildcards.kmer,
cpus = '1',
mem = '6G',
gpus = '0',
walltime = '00:30:00'
log:
'logs/'+config['input_folder']+'/kmers/{kmer}/{id}/calcKmerErrorRates.log'
conda:
......
......@@ -123,9 +123,9 @@ rule estimateErrorRates:
params:
# cluster execution
cpus = '1',
mem = '32G',
mem = '1G',
gpus = '0',
walltime = '00:30:00'
walltime = '00:10:00'
conda:
'../envs/biopythonworkbench.yaml'
script:
......@@ -154,7 +154,12 @@ rule calcKmerStats:
stats = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/stats.tsv'
params:
id = lambda wildcards: wildcards.id,
k = lambda wildcards: wildcards.kmer
k = lambda wildcards: wildcards.kmer,
# cluster execution
cpus = '1',
mem = '2G',
gpus = '0',
walltime = '00:30:00'
conda:
'../envs/biopythonworkbench.yaml'
log:
......
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