Some Busco errors are silently ignored

[muffato]

#147 highlighted that the nf-core module runs Busco in "batch mode", which makes Busco ignore many runtime errors.
Although this is OK for Prodigal failing to find any gene, what about the other errors ? There are many places in the code than can raise a BuscoError exception. Are they really OK to ignore ?

[tkchafin]

At least for the Prodigal failure, ignoring it leads to a false output that there were no genes matching, so at least for that case silently catching the error yields an incorrect result

[muffato]

Sure, but for Prodigal it's actually what Rich wanted

[muffato]

I can confirm there is a problem. If I delete the *cutoff files from the Busco database, the problem is internally caught by Busco and reported in the output file

GCA_922984935.2.subset.phiXspike.fasta  Run failed; check logs

while returning an exit code of 0.

The pipeline doesn't recognise there's an error and runs the following steps RESTRUCTUREBUSCODIR and BLOBTOOLKIT_EXTRACTBUSCOS:

[dc/79ba75] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BUSCO_BUSCO (GCA_922984935.2_archaea_odb10)                [100%] 10 of 10 ✔
[5d/47ec0a] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:RESTRUCTUREBUSCODIR (GCA_922984935.2_archaea_odb10)        [100%] 10 of 10 ✔
[b9/b49b4f] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:BLOBTOOLKIT_EXTRACTBUSCOS (GCA_922984935.2)                [100%] 1 of 1 ✔
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:BUSCO_DIAMOND:DIAMOND_BLASTP                                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:BLOBTOOLKIT_CHUNK                                             -
[-        ] process > SANGERTOL_BLOBTOOLKIT:BLOBTOOLKIT:RUN_BLASTX:DIAMOND_BLASTX                                                -

It doesn't go further than BLOBTOOLKIT_EXTRACTBUSCOS because the latter can't find any gene to extract and outputs an empty file, which doesn't pass the test https://github.com/sanger-tol/blobtoolkit/blob/0.8.0/subworkflows/local/busco_diamond_blastp.nf#L166-L168