avoid misleading sample-sheet errors on unrelated pipeline abort (#1629)

[asp8200]

Some code from Claude to fix #1629

I checked that the fix works in Sarek v3.9.0. (For reasons, I can't easily check that the fix works with dev.)

My tests:

$ sarek -profile test_full --snpeff_cache /ngc/people/andped/test_sarek

and that gave me the following on stdout:

[-        ] NFCORE_SAREK:PREPARE_GENOME:UNZIP_ALLELES                         -
[-        ] NFCORE_SAREK:PREPARE_GENOME:UNZIP_LOCI                            -
[-        ] NFCORE_SAREK:PREPARE_GENOME:UNZIP_GC                              -
[-        ] NFCORE_SAREK:PREPARE_GENOME:UNZIP_RT                              -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED               -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT    -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED -
[-        ] NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_ANTITARGET           -
[-        ] NFCORE_SAREK:PREPARE_REFERENCE_CNVKIT:CNVKIT_REFERENCE            -
Path provided with SnpEff cache is invalid.
Make sure there is a directory named GRCh38.115 in /ngc/people/andped/test_sarek.
Please refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.
$ 

The log-file .nextflow.logalso looks fine:

$ grep "Path provided with SnpEff cache is invalid" .nextflow.log
Jul-22 10:33:57.488 [main] DEBUG nextflow.Session - Session aborted -- Cause: Path provided with SnpEff cache is invalid.
nextflow.exception.WorkflowScriptErrorException: Path provided with SnpEff cache is invalid.
$ grep "The sample-sheet only contains" .nextflow.log
$

Next, I checked that the samplesheet-error-message is still given when needed, that is, I ran

$ sarek -profile test_full --input only_normal.csv --tools ascat

and I got

The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ascat

Those tests were done with the fix in Sarek v3.9.0. I expect the same results with the fix on dev.

[asp8200]

As expected, the sentieon-related tests are failing due to missing sentieon license file. If you want, I can perhaps make this PR from the nf-core/sarek-repo instead of my sarek-fork. That should fix the issue with missing sentieon license file.

[famosab]

As expected, the sentieon-related tests are failing due to missing sentieon license file. If you want, I can perhaps make this PR from the nf-core/sarek-repo instead of my sarek-fork. That should fix the issue with missing sentieon license file.

I would suggest to do exactly that :) and in the future you can just work on a branch in the repo directly instead of forking!