Quilt use sample name as input

[LouisLeNezet]

Description of the bug

If the name of the sample in the bam files are equal QUILT will generate a wrongly formatted vcf with multiple times the same sample names, leading in an error in bcftools annotate step.
We need to provide a sampleNames_file in the same order as the bamlist.

Command used and terminal output

Relevant files

No response

System information

No response