Potentially incompatible outputs are generated with BAM output and Spark MarkDuplicates

[lbeltrame]

Description of the bug

Discussed with @maxulysse on Slack:

1. Spark MarkDuplicates wants name sorted output, so BAMs are made as such
2. If requesting BAM output instead of CRAM, merging happens with name sorted output, causing non-contiguous blocks to be close to each other
3. Indexing of the merged BAM fails

The options should be made mutually exclusive so that broken output is not generated.

Command used and terminal output

nextflow run nf-core/sarek -r 3.5.1 --input samplesheet.csv -params-file parameters.yaml --outdir ./ -profile cluster -qs 2 -resume --igenomes_ignore

Relevant files

parameters.zip

nextflow-log.zip

System information

• Nextflow version: 24.10.2
• Hardware: HPC
• Executor: SLURM
• Container engine: Apptainer
• OS: Debian 10