Commit a8b82c61 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

try 3 incorp master

parent 74fa282a
......@@ -9,4 +9,5 @@ benchmarks/
logs/
report/
*.sif
hilbert/
\ No newline at end of file
hilbert/
.vscode/
\ No newline at end of file
......@@ -60,6 +60,7 @@ def extractTsvValue(filePath,line,nolabels=False):
return lines[line].split('\t')[0] if nolabels else lines[line].split('\t')[1]
ruleorder: calcLikelihoods_master > calcLikelihoods
rule calcLikelihoods:
input:
expected = 'data/auxiliary/{dataset}/kmers/{kmer}/{id}/expected_counts.json',
......@@ -72,7 +73,6 @@ rule calcLikelihoods:
likelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/likelihoods_cov.json',
unexpectedLikelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json'
#diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv'
priority: 0
log:
'logs/{dataset}/{iterset}/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log'
benchmark:
......@@ -102,7 +102,6 @@ rule calcLikelihoods_master:
likelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/likelihoods_cov.json',
unexpectedLikelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json'
#diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv'
priority: 1
log:
'logs/{dataset}/master/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log'
benchmark:
......@@ -111,7 +110,7 @@ rule calcLikelihoods_master:
e = (lambda wildcards,input : extractTsvValue(input.kmerError,0)),
deviationCutoff = (lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))),
#cluster exectuion
cpus = '1',
cpus = '4',
mem = '4G',
gpus = '0',
walltime = '01:30:00'
......
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