[BUG] bwa index not work correctly

[jianhong]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/module documentation

Description of the bug

bwa index create indexes at working folder but not bwa subfolder as before under conda environment. (previous it works)

System

• Hardware: MAC book
• Executor: local
• OS: macOS Big Sur
• Version: 11.4

Nextflow Installation

• Version: 21.05.0-edge.5563

Container engine

• Engine: Conda
• version: 4.9.2
• Image tag: nf-core/tools version 2.0.1.dev0

Additional context

It can be fixed by change bwa/index/main.nf line 32

bwa index $options.args $fasta -p bwa/${fasta.baseName}

to

bwa index $options.args -p bwa/${fasta.baseName} $fasta

[SPPearce]

Closing as outdated