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nf-core

And a related question. I want to specify a temporary path to Spades when running the assembly. The lines to write at `nextflow.config` should be these ones no:
```withName: SPADES {
    ext.args = ['--tmp-dir', '\$LUSTRE_SCRATCH']
    }```
I am running the processes in SLURM. The variable $LUSTRE_SCRATCH is defined by SLURM, and I doubt how to do it efficiently. Hypothetically, sending it this way should be correct?

Not sure if the list part works without joining. :thinking_face: I would write:
```withName: SPADES {
  ext.args = "-tmp-dir \$LUSTRE_SCRATCH --${params.spades_flavor"
}```
The `params.spades_flavor` is there to make sure that that parameter works. Otherwise you get the default flavour of Spades.
Check how `.command.sh`  in the process work directory looks if something didn't work.