feat: add test_hybrid snapshot

[dialvarezs]

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[nf-core-bot]

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[jfy133]

Overall LGTM, I only noticed missing files:

• GenomeBinning/QC/busco_summary.tsv
• GenomeBinning/QC/quast_bin_summary.tsv
• GenomeBinnig/SemiBin2/log/SPAdesHybrid-SemiBin2-minigut.SemiBinRun.log (but covered by other files really)

Other observations:

• There are no Chopper output files when I run the test profile itself, is that expected? There is just an empty directory
• QC_longreads/samtools/stats/minigut_null.stats the null looks funky

[d4straub]

Hi,

I had an issue with the hybrid assembly, see #1031. This test here would not cover it but would need at least 2 samples and coassembly_group = true. I tested the solution in #1031 (comment) and RAM requirements were on my laptop still small, so I assume that would work.
The question is, would be extending this test be a solution or rather make a new test? I have the impression a new test would cover only whats done here already and more (i.e. duplicate this test unnecessarily). Therefore I suggest to extend test_hybrid.

[dialvarezs]

I improved this snapshot addressing everything that came up:

@jfy133

Files...

• GenomeBinning/QC/busco_summary.tsv: BUSCO summary is not stable, that's why we're excluding it in the snapthots, but we check that is a valid CSV and that the row count is stable, and also we have bin_summary snapshotted, and BUSCO info is contained there. So I guess it's ok.
• GenomeBinning/QC/quast_bin_summary.tsv: it was always there
• GenomeBinnig/SemiBin2/log/SPAdesHybrid-SemiBin2-minigut.SemiBinRun.log (but covered by other files really)
  Other observations. Yep, this is not stable because it has timestamp, but we check that the logs have the finishing line.

There are no Chopper output files when I run the test profile itself, is that expected?

Yeah, by default qc filtered FASTQs are not published, and Chopper only publishes that (not even a log). I enabled the FASTQ publishing, so it's not empty now.

QC_longreads/samtools/stats/minigut_null.stats the null looks funky

It was using the wrong meta key, it's fixed now

@d4straub

I added a new samplesheet with 2 samples with short and long reads, and enabled co-assembly. Without your fix it was failing, but now it's working.

[d4straub]

Perfect, thanks!

[d4straub]

This looks good to me actually.
Maybe @jfy133 still finds something missing? :)