Hi yall The pipeline is not saving the cram or bam files, even though I have the

--save_mapped

and

--save_output_as_bam

OUT_BASE="./results"


    # Run Sarek with Parabricks
    nextflow run nf-core/sarek \
        -r 3.8.1 \
        -profile docker,gpu \
        --input samplesheet_lpwgs.csv \
        --outdir "${OUT_BASE}/lpwg" \
        --ref ../genome/GRCh38.primary_assembly.genome.fa \
        --use_parabricks \
        --aligner parabricks \
        --save_output_as_bam \
        --save_mapped \
        -c custom-parabricks.config

I was expecting the

converted

directory in the results folder, but it does not exist. The

results/lpwg/preprocessing/parabricks/

contains directories for each sample, but they're empty. I don't get any errors. And the multiqc report seems normal. I am running 3.8.1 on N E X T F L O W ~ version 25.10.4

@Famke Bäuerle any clue?

I have tested with a single-lane sample and with a mutlilane sample with the same result. I also tried it with singularity instead of docker - no difference.

I am wondering if it could be due to save_mapped and save_output_as_bam. I have a feeling that might not work with parabricks, asking famke as she's our resident expert on all things parabricks

I'll try with out those flags, but I need bams, not crams. As far as I know, FQ2BAM defaults to outputting crams

yes its a known bug

Removing the save_as_bam actually resulted in a cram file being saved in the parabricks dir.