sarek
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BWA index isn't coppied over with using save-reference option
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
Not sure I understand. When setting --save_reference
it is intended that the bwa index should be saved. Can you elaborate on the issue?
Sorry meant to say is not coppied over.