Fix hybrid co-assembly with SPAdes

[d4straub]

Fix #1031

Essentially, meta.single_end was missing for long reads that were about to be pooled with POOL_LONG_READS (that is the nf-core module CAT_FASTQ). This is added here at the appropriate point.

Afaik there is no test config that makes sure that problem is tested.

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• This comment contains a description of changes (with reason).
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[jfy133]

LGTM, but could you add a test 😅, now that we have the testing framework implemented:)

[d4straub]

but could you add a test

Hm, well, test_hybrid is almost there, that is already in the work in #1029. coassemble_group = true and a second sample is missing though to catch that issue. Currently there is no second long reads file in mag test datasets.

I'm going to test how much resources SPAdes hybrid co-assembly needs with the data as described in #1031 (comment).
Edit: resources seem no issue!

[jfy133]

but could you add a test

Hm, well, test_hybrid is almost there, that is already in the work in #1029. coassemble_group = true and a second sample is missing though to catch that issue. Currently there is no second long reads file in mag test datasets.

I'm going to test how much resources SPAdes hybrid co-assembly needs with the data as described in #1031 (comment).
Edit: resources seem no issue!

If we are still building it, now would be the time to tweak it to at the second sample (imo)!

[dialvarezs]

I'm doing the setup to test co-assembly + hybrid and I reproduced the issue.
I'm going to merge this now, and follow-up in the hybrid snapshot PR with the updated samplesheet and profile to cover this.