fix error when emtpy fusioninspector tsv

[atrigila]

Closes #796

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[grst]

Hi @atrigila,

I've tried running this PR on our dataset, and it fails with

Join mismatch for the following entries: 
- key=[id:Homo_sapiens_GRCh38_46_dna_primary_assembly.fa] values= 
- key=[id:Homo_sapiens_GRCh38_46_dna_primary_assembly.fa.fai] values=

doesn't seem to be related to the vcf_collect changes directly, but probably rather the recent template update?

[grst]

CC @apeltzer

[apeltzer]

Looks like a good approach to me, keeping the table structure the same

[nvnieuwk]

One small question but looking good to me! This was also bugging me so thanks for the fix

[apeltzer]

Hi @atrigila,

I've tried running this PR on our dataset, and it fails with

Join mismatch for the following entries: 
- key=[id:Homo_sapiens_GRCh38_46_dna_primary_assembly.fa] values= 
- key=[id:Homo_sapiens_GRCh38_46_dna_primary_assembly.fa.fai] values=

doesn't seem to be related to the vcf_collect changes directly, but probably rather the recent template update?

Only remaining issue is this one - any idea @nvnieuwk ? Sounds like an issue with the latest template I'm afraid :-(

[nvnieuwk]

@grst could you post the full log of the run here?

[apeltzer]

WARN: Skipping COSMIC DB download from `FUSIONREPORT_DOWNLOAD` and skip using it in `FUSIONREPORT`
Uploading local `bin` scripts folder to s3://redacted/bin
Monitor the execution with Seqera Platform using this URL: https://redacted
Join mismatch for the following entries:
- key=[id:Homo_sapiens_GRCh38_46_dna_primary_assembly.fa] values=
- key=[id:Homo_sapiens_GRCh38_46_dna_primary_assembly.fa.fai] values=
-[nf-core/rnafusion] Pipeline completed with errors-
WARN: Unable to upload nextflow out file: nf-dbvWHYOOca7e0.txt — reason: Thread was interrupted
WARN: Unable to upload nextflow log file: nf-dbvWHYOOca7e0.log — reason: Thread was interrupted
WARN: Unable to upload nextflow timeline file: timeline-dbvWHYOOca7e0.html — reason: Thread was interrupted
WARN: Unable to upload tower reprts file: nf-dbvWHYOOca7e0-reports.tsv — reason: Thread was interrupted
ERROR ~ Pipeline failed. Please refer to troubleshooting docs for common issues: https://nf-co.re/docs/running/troubleshooting
-- Check 'nf-dbvWHYOOca7e0.log' file for details
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details

Thats it I'm afraid :-(

[grst]

I confirm this works in combination with #806. Feel free to go ahead and merge.