Commit ba76f0a8 authored by Jan Hoeckesfeld's avatar Jan Hoeckesfeld
Browse files

Merge branch 'iterationset-tests-experimental' into hilbert-hpc

parents 12e9e78a a8b82c61
...@@ -21,3 +21,7 @@ config.yaml ...@@ -21,3 +21,7 @@ config.yaml
*.simg *.simg
*.sif *.sif
hilbert/ hilbert/
<<<<<<< HEAD
=======
.vscode/
>>>>>>> iterationset-tests-experimental
...@@ -60,6 +60,7 @@ def extractTsvValue(filePath,line,nolabels=False): ...@@ -60,6 +60,7 @@ def extractTsvValue(filePath,line,nolabels=False):
return lines[line].split('\t')[0] if nolabels else lines[line].split('\t')[1] return lines[line].split('\t')[0] if nolabels else lines[line].split('\t')[1]
ruleorder: calcLikelihoods_master > calcLikelihoods
rule calcLikelihoods: rule calcLikelihoods:
input: input:
expected = 'data/auxiliary/{dataset}/kmers/{kmer}/{id}/expected_counts.json', expected = 'data/auxiliary/{dataset}/kmers/{kmer}/{id}/expected_counts.json',
...@@ -72,7 +73,6 @@ rule calcLikelihoods: ...@@ -72,7 +73,6 @@ rule calcLikelihoods:
likelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/likelihoods_cov.json', likelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/likelihoods_cov.json',
unexpectedLikelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json' unexpectedLikelihoods = 'data/auxiliary/{dataset}/{iterset}/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json'
#diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv' #diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv'
priority: 0
log: log:
'logs/{dataset}/{iterset}/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log' 'logs/{dataset}/{iterset}/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log'
benchmark: benchmark:
...@@ -102,7 +102,6 @@ rule calcLikelihoods_master: ...@@ -102,7 +102,6 @@ rule calcLikelihoods_master:
likelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/likelihoods_cov.json', likelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/likelihoods_cov.json',
unexpectedLikelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json' unexpectedLikelihoods = 'data/auxiliary/{dataset}/master/kmers/{kmer}/{id}/unexpected_likelihoods_cov.json'
#diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv' #diffs = 'data/auxiliary/kmers/{kmer}/{id}/kmer_diff.tsv'
priority: 1
log: log:
'logs/{dataset}/master/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log' 'logs/{dataset}/master/probabilistic/kmers/{kmer}/{id}/likelihoods_cov.log'
benchmark: benchmark:
...@@ -111,7 +110,7 @@ rule calcLikelihoods_master: ...@@ -111,7 +110,7 @@ rule calcLikelihoods_master:
e = (lambda wildcards,input : extractTsvValue(input.kmerError,0)), e = (lambda wildcards,input : extractTsvValue(input.kmerError,0)),
deviationCutoff = (lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))), deviationCutoff = (lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))),
#cluster exectuion #cluster exectuion
cpus = '1', cpus = '4',
mem = '4G', mem = '4G',
gpus = '0', gpus = '0',
walltime = '01:30:00' walltime = '01:30:00'
......
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