[FEATURE] Early failure for non-existent sdrf files

[fabianegli]

The following invocation of the quantms pipeline should complain about the non-existence of the SDRF file instead of the missing protein database

% nextflow run bigbio/quantms --input non_existent_input_sdrf_file.csv

 N E X T F L O W   ~  version 25.04.7

Launching `https://github.com/bigbio/quantms` [infallible_pauling] DSL2 - revision: e516ddca04 [master]

[-        ] BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK        -
[-        ] BIGBIO_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRF_PARSING    -
[-        ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:DECOMPRESS          -
[-        ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_INDEXING       -
[-        ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:THERMORAWFILEPARSER -
[-        ] BIGBIO_QUANTMS:QUANTMS:FILE_PREPARATION:MZML_STATISTICS     -
ERROR ~ No protein database provided

 -- Check '.nextflow.log' file for details

[jpfeuffer]

I think I disagree with this one.
Existence of required parameters should be checked before existence of provided files.

[ypriverol]

@fabianegli thanks a lot for been back. More than happy to review a PR from you solving this issue ;) If not, I will try to allocate some time next week.

[ypriverol]

I actually think we should complain about both, the database and the sdrf in one go.

[jpfeuffer]

I don't think it's worth the trouble. You would need to collect all possible errors from both steps over which we might not even have control because they may be nextflow/nf-core controlled.
But if someone really really needs it for solving all the problems at once, be my guest, but please think about the maintenance cost.

[fabianegli]

@jpfeuffer I see your point and think it is valid. I think we can close it as works as intended.

The only thin is that I would love to have with such an error also a note about the actual CLI printed for assistance. But that's a different issue.