jacorvar

Dear all, has it already been implemented? I've just tried to integrate miRNA expression and methylation data by means of TCGAvisualize_starburst function but it struggles with miRNA IDs and prompts...

@torongs82 Have you already had a look at this issue?

> The bus error would just be java crashing. > > @jacorvar do I understand correctly that this is the local executor in a single node slurm job where you...

Are there no other alternatives? I tried other pipelines from nf-core and got no errors on my current HPC. Besides, it's only the `BaseRecalibrator` step which complains, while everything works...

After using the slurm executor and `--no_intervals` option there are less errors specifically at the `prepare_recalibration` step. when running it individually. However, I've noticed `sarek` does not cache at all...

Is there anything I can do to enable caching at that step? I'm running the following inside a script with slurm: ``` export NXF_OPTS='-Xms1g -Xmx4g' export NXF_EXECUTOR=slurm ulimit -u 4126507...

OK, that works now BTW, given that I must provide the gene sequence instead of the whole genome/chromosome sequence in order to anchor the trace, which strategy would you suggest...