BWA index isn't coppied over with using save-reference option

[vsmalladi]

Description of the bug

BWA index isn't copied over with using save-reference option on Azure. This is because it needs files in the path to copy over.

Can be fixed with updating the index modules: https://github.com/nf-core/modules/pull/1964

Command used and terminal output

./nextflow run .nextflow/assets/nf-core/sarek/main.nf -c azure.config -w "az://genomas-raros/work" --outdir "az://genomas-raros/results"  --tools haplotypecaller --input sarek.csv --igenomes_ignore --save_reference --genome 'custom'

Relevant files

No response

System information

• nextflow version 22.04.5.5708
• Azure VM
• Executor Azure
• Docker
• OS Ubuntu
• 3.0.1

[FriederikeHanssen]

Not sure I understand. When setting --save_reference it is intended that the bwa index should be saved. Can you elaborate on the issue?

[vsmalladi]

Sorry meant to say is not coppied over.