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

changed resources

parent b8901a18
...@@ -12,8 +12,8 @@ rule estimateKmerCoverage: ...@@ -12,8 +12,8 @@ rule estimateKmerCoverage:
#cluster execution #cluster execution
cpus = '1', #TODO: This could in theory be sped up significantly using a shared cache and multithreading cpus = '1', #TODO: This could in theory be sped up significantly using a shared cache and multithreading
gpus = '0', gpus = '0',
mem = '64G', mem = '6G',
walltime = '00:45:00' walltime = '00:10:00'
log: log:
'logs/' + config['input_folder'] + '/kmers/{kmer}/{id}/estimateKmerCoverage.log' 'logs/' + config['input_folder'] + '/kmers/{kmer}/{id}/estimateKmerCoverage.log'
benchmark: benchmark:
......
...@@ -82,9 +82,9 @@ rule bwa: ...@@ -82,9 +82,9 @@ rule bwa:
params: params:
#cluster execution #cluster execution
cpus = '1', cpus = '1',
mem = '32G', mem = '1G',
gpus = '0', gpus = '0',
walltime = '00:30:00' walltime = '00:10:00'
singularity: singularity:
'docker://biocontainers/bwa:v0.7.17-3-deb_cv1' 'docker://biocontainers/bwa:v0.7.17-3-deb_cv1'
shell: shell:
...@@ -358,7 +358,11 @@ rule calcKmerErrorRates: ...@@ -358,7 +358,11 @@ rule calcKmerErrorRates:
output: output:
error = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/error_estimate.txt' error = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/error_estimate.txt'
params: params:
k = lambda wildcards: wildcards.kmer k = lambda wildcards: wildcards.kmer,
cpus = '1',
mem = '6G',
gpus = '0',
walltime = '00:30:00'
log: log:
'logs/'+config['input_folder']+'/kmers/{kmer}/{id}/calcKmerErrorRates.log' 'logs/'+config['input_folder']+'/kmers/{kmer}/{id}/calcKmerErrorRates.log'
conda: conda:
......
...@@ -123,9 +123,9 @@ rule estimateErrorRates: ...@@ -123,9 +123,9 @@ rule estimateErrorRates:
params: params:
# cluster execution # cluster execution
cpus = '1', cpus = '1',
mem = '32G', mem = '1G',
gpus = '0', gpus = '0',
walltime = '00:30:00' walltime = '00:10:00'
conda: conda:
'../envs/biopythonworkbench.yaml' '../envs/biopythonworkbench.yaml'
script: script:
...@@ -154,7 +154,12 @@ rule calcKmerStats: ...@@ -154,7 +154,12 @@ rule calcKmerStats:
stats = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/stats.tsv' stats = 'data/auxiliary/'+config['input_folder']+'/kmers/{kmer}/{id}/stats.tsv'
params: params:
id = lambda wildcards: wildcards.id, 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: conda:
'../envs/biopythonworkbench.yaml' '../envs/biopythonworkbench.yaml'
log: log:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment