Emilio Palumbo

@thasso I also have the `-b` option in our SGE (univa 8.2 as you can see below): ``` $ gsub -help UGE 8.2.0 usage: qsub [options] ... [-b y[es]|n[o]] handle...

Hi, apologies for the late reply. I see the issue and I think we can add the support to run STAR with multiple lanes fastqs as you suggest. You should...

Hi all, to introduce myself, I am in the Nextflow team and also taking part in the GA4GH Large Scale Genomics work stream. I tend to believe that implementation-specific resources...

For the moment, just adding a `--read-strand` option to enforce a specific strandness to all processed samples. By default the option is empty (`''`) and the pipeline will infer strandness...

Hi Paul, apologies for the late reply. About `mergeBam` not always working, I suspect it is related to the open issue #48. I am going to fix it soon. About...

HI Paul, I could not find anything useful in the logs. Did you run the `.command.run` and `.command.sh` locally or submitted via `slurm`? I am wondering whether the problem is...

Hi Paul, could you please try running the pipeline with the included small test dataset and the `markdup` profile? E.g.: ``` nextflow run grape-nf -profile markdup -with-singularity ``` Does the...

Hi Paul, thanks, that does not help much. I just realized you are not using the latest version of Nextflow. Any chance you can make a test using that version?...

Hi Paul, it's a weird issue and it's hard to tell what's the cause. Maybe removing some of the complexity would help. Could you try running it without `Singularity` (e.g....

Hi Paul, any news regarding this issue? Best, Emilio