Integer 0 value for `lane` column in samplesheet causes pipeline to break

[serenalotreck]

Description of the bug

If the lane value in the samplesheet is 0, pipeline throws a Missing or unknown field in csv file header. Please check your samplesheet error. Changing the value to a string like L1 resolves the issue.

Command used and terminal output

nextflow run nf-core/sarek \
    -profile conda \
    --input samples.csv \
    --outdir output

EDIT adding error message:

Missing or unknown field in csv file header. Please check your samplesheet
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-

Relevant files

This error happens after any error caused by the fastq files not existing. Rather than also upload my fastq files, I've attached a samplesheet here that, when fastq_1 and fastq_2` are filled in with real files should reproduce the error.

samplesheet.csv

System information

• Nextflow version: 24.10.2.5932
• Hardware: HPC
• Executor: Executing on a dev node
• Container enine: conda
• OS: Ubuntu 22.04
• nf-core/sarek version: 3.5.1

[maxulysse]

I have a fix in #1924