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A number of users have reported that the RSeQC tin.py module added in v3.4 is causing issues - mainly due to very long run-times. By default, the module has a label of process_medium which means it runs for 8 hours but is still failing. I don't think it makes sense to have such a long running QC step on by default in the pipeline and as such it should be opt-in rather than set by default.
Once it has been removed you can run tin.py by appending tin to the --rseqc_modules parameter like below:
Description of feature
A number of users have reported that the RSeQC
tin.py
module added in v3.4 is causing issues - mainly due to very long run-times. By default, the module has a label ofprocess_medium
which means it runs for 8 hours but is still failing. I don't think it makes sense to have such a long running QC step on by default in the pipeline and as such it should be opt-in rather than set by default.Once it has been removed you can run
tin.py
by appendingtin
to the--rseqc_modules
parameter like below:--rseqc_modules 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication,tin'
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