Allow custom assembly options and export assembly QC

[d4straub]

• added exit code 247 to bowtie2 retry, 247 is when it runs out of memory while index building
• added two parameters (--spades_options & --megahit_options) to allow custom SPAdes and MEGAHIT options, this is required to adjust e.g. k-mers or presets for more challenging assemblies
• export bowtie2 mapping statistics as another important QC. This is nicely integrated into the MultiQC report when assembling individual samples but not when assembling groups. Because it is here impossible to match assembly to sample and would create a huge mess.
• docs are updated

edit: Just figured out that MEGAHIT told Process megahit (groupall) terminated with an error exit status (250) when running into RAM issues. That should be added as well. Unfortunately, time limits resulted in an empty error code, very unfortunate.
edit2: Re-try MEGAHIT when exiting with code 250

[skrakau]

Regarding the time limit and the missing exit code, can it be a Nextflow or slurm problem if this is not reported properly? See e.g. nextflow-io/nextflow#1354

Didn't it work in the past?

[skrakau]

Still, I think in general this way of allowing general custom options as strings is not ideal, we should fix those as soon as possible.

[d4straub]

Regarding the time limit and the missing exit code, can it be a Nextflow or slurm problem if this is not reported properly? See e.g. nextflow-io/nextflow#1354
Didn't it work in the past?

edit: Sorry, was too fast here, sure that might be. Sometimes it works for me, sometimes it doesnt.

Still, I think in general this way of allowing general custom options as strings is not ideal, we should fix those as soon as possible.

True, but I am not certain at this point which options might be most helpful.