Mapped bam and bai published in different folders

[asp8200]

trafficstars

Description of the bug

When running

nextflow run nf-core/sarek -profile test,alignment_to_fastq,docker -r 3.4.2 --outdir results --save_mapped --save_output_as_bam

I get

results/preprocessing/mapped/test/test-1.sorted.bam.bai
results/preprocessing/mapped/test-1/test-1.sorted.bam

I think the bam and bai sound be in the same folder.

Command used and terminal output

nextflow run nf-core/sarek -profile test,alignment_to_fastq,docker -r 3.4.2 --outdir results --save_mapped --save_output_as_bam

results/preprocessing/mapped/test/test-1.sorted.bam.bai
results/preprocessing/mapped/test-1/test-1.sorted.bam

Relevant files

No response

System information

No response

[asp8200]

Seems to work fine if I drop --save_output_as_bam, that is, it works for

nextflow run nf-core/sarek -profile test,alignment_to_fastq,docker -r 3.4.2 --outdir results --save_mapped 

[FriederikeHanssen]

closed as fixed