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Jan Hoeckesfeld
Snakemake Ngs Spa Typing
Commits
16d936e2
Commit
16d936e2
authored
Feb 09, 2021
by
Jan Hoeckesfeld
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revert previous change
parent
04c5a8cb
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rules/probabilistic.smk
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16d936e2
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@@ -86,10 +86,10 @@ rule calcLikelihoods:
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@@ -86,10 +86,10 @@ rule calcLikelihoods:
gpus = '0',
gpus = '0',
walltime = lambda wildcards, attempt: '01:00:00'
walltime = lambda wildcards, attempt: '01:00:00'
singularity:
singularity:
lambda wildcards: 'docker://phspo/ckmertools:latest' if wildcards.iterset=="master" else
'singularity_container/ckmertools_iterset.sif'
'singularity_container/ckmertools_iterset.sif'
#'docker://phspo/ckmertools:iterationset-tests'
#'docker://phspo/ckmertools:iterationset-tests'
shell:
shell:
lambda wildcards: 'c_kmertools --e {input.expected} --c {params.cpus} --m 0 --o {input.observed} --kmererror {params.e} --d {params.deviationCutoff} --target {output.likelihoods} --unexpected {output.unexpectedLikelihoods} --log {log}' if wildcards.iterset=="master" else
'c_kmertools --e {input.expected} --c {params.cpus} --m 0 --o {input.observed} --kmererror {params.e} --d {params.deviationCutoff} --target {output.likelihoods} --unexpected {output.unexpectedLikelihoods} --log {log} --itersetType {params.itersetType} --hammingdist {input.V_kmers_distances} --kmersindex {input.V_kmers}'
'c_kmertools --e {input.expected} --c {params.cpus} --m 0 --o {input.observed} --kmererror {params.e} --d {params.deviationCutoff} --target {output.likelihoods} --unexpected {output.unexpectedLikelihoods} --log {log} --itersetType {params.itersetType} --hammingdist {input.V_kmers_distances} --kmersindex {input.V_kmers}'
rule calcLikelihoods_Generative:
rule calcLikelihoods_Generative:
...
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