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Jan Hoeckesfeld
Snakemake Ngs Spa Typing
Commits
b9c64be2
Commit
b9c64be2
authored
Feb 08, 2021
by
Jan Hoeckesfeld
Browse files
workflow bugs
parent
f4f0bd06
Changes
3
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Snakefile
View file @
b9c64be2
...
...
@@ -8,16 +8,21 @@ configfile: "config.yaml"
validate(config, "schemas/config.schema.yaml")
#Generate Input/Output Files from specified folder
def get_input_ids():
inputIDs, = glob_wildcards('data/input/'+wildcards.dataset+'/{id}'+config["datasets"][wildcards.dataset]['input_read_1_ending'])
return inputIDs
#Generate Input/Output Files from specified folder
kmer_lengths = config['kmers']
dataset_inputIDs = {}
for d in config['datasets'].keys():
inputIDs = get_input_ids()
dataset_inputIDs[d] = [str(x) for x in inputIDs]
#kmer_lengths = [24]
def get_general_inputs(wildcards):
run_dir = wildcards.dataset
inputIDs, = glob_wildcards('data/input/'+wildcards.dataset+'/{id}'+config["datasets"][wildcards.dataset]['input_read_1_ending'])
dataset_inputIDs[wildcards.dataset] = inputIDs
inputIDs = get_input_ids()
possible_params = {
'assembly_model': expand('data/output/'+run_dir+'/{id}/exactMatches.tsv',id=inputIDs),
...
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@@ -57,6 +62,12 @@ rule run_dataset:
summarys = expand('data/auxiliary/{dataset}/{iterset}_summary.md', iterset=use_itersets(), allow_missing=True)
output:
summary = 'data/output/{dataset}_summary.md'
params:
# cluster execution
cpus = '1',
mem = '1G',
gpus = '0',
walltime = '00:01:00'
# TODO create summary
shell:
'touch {output.out}'
...
...
@@ -66,6 +77,12 @@ rule run_iterset:
get_iterset_inputs
output:
out = 'data/auxiliary/{dataset}/{iterset}_summary.md'
params:
# cluster execution
cpus = '1',
mem = '1G',
gpus = '0',
walltime = '00:01:00'
# TODO create summary
shell:
'touch {output.out}'
...
...
clusterExecution.sh
View file @
b9c64be2
...
...
@@ -24,5 +24,5 @@ mkdir -p clusterLogs
type
snakemake
>
/dev/null 2>&1
||
{
echo
>
&2
"I require snakemake but it's not installed or added to your path. Aborting..."
;
exit
1
;
}
snakemake
--jobs
$maxNrOfConcurrentJobs
--use-singularity
--use-conda
--reason
--jobscript
cluster/jobscript.sh
--cluster
"qsub -e clusterLogs/{rule}.{wildcards}.{jobid}.errors -o clusterLogs/{rule}.{wildcards}.{jobid}.output -A
${
projectID
}
-l select=1:ncpus={params.cpus}:ngpus={params.gpus}:mem={params.mem} -l walltime={params.walltime}"
--restart-times
3
--envvars
SINGULARITY_CACHEDIR
snakemake
--jobs
$maxNrOfConcurrentJobs
--use-singularity
--use-conda
--reason
--jobscript
cluster/jobscript.sh
--cluster
"qsub -e clusterLogs/{rule}.{wildcards}.{jobid}.errors -o clusterLogs/{rule}.{wildcards}.{jobid}.output -A
${
projectID
}
-l select=1:ncpus={params.cpus}:ngpus={params.gpus}:mem={params.mem} -l walltime={params.walltime}"
--restart-times
3
rules/probabilistic.smk
View file @
b9c64be2
...
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@@ -77,14 +77,14 @@ rule calcLikelihoods:
benchmark:
'benchmarks/{dataset}/{iterset}/probabilistic/kmers/{kmer}/{id}/calcLikelihoodsCoverageBasedModel.txt'
params:
e =
(
lambda wildcards,input : extractTsvValue(input.kmerError,0)
)
,
deviationCutoff =
(
lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config))
)
,
e = lambda wildcards,input : extractTsvValue(input.kmerError,0),
deviationCutoff = lambda wildcards,input : round(config['deviationCutoff']*extractCoverageEstimateFile(input.kmerCoverageEstimate,config)),
itersetType = lambda wildcards: wildcards.iterset,
#cluster exectuion
cpus =
lambda wildcards, attempt: str(2*attempt)
,
cpus =
'4'
,
mem = '10G',
gpus = '0',
walltime = lambda wildcards, attempt: '0
' + str(attempt) + '
:00:00'
walltime = lambda wildcards, attempt: '0
1
:00:00'
singularity:
'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
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