BUG: BWA-MEM wrapper - Passing command line argument -O in extra triggers wrapper cancel

[KuechlerO]

Hello guys,
I stumbled over an unexpected behaviour for the wrapper BWA MEM - v1.17.3/bio/bwa/mem:

Snakemake version
7.12.1

Describe the bug
Including the command line argument -O with any INT as passed value is causing the cancelation of the called wrapper. It seems that -O is protected somehow. However, it is a valid argument for the "BWA MEM" algorithm.

Print-out on command line: You have specified output format (-O/--output-fmt) in params.extra; this is automatically infered from output file extension.

Logs

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 50
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=204800, disk_mb=15169, cpus=50, time_min=360
Select jobs to execute...

[Tue Oct 25 20:39:25 2022]
rule bwa_mem_custom2:
    input: /sc-scratch/sc-scratch-btg/olik_splicing_project/splice-prediction/snakemake_workflows/Snakemake_Main/output/module1_qc_preproc_and_alignment/output/trimmomatic/76664_R1.fastq.gz, /sc-scratch/sc-scratch-btg/olik_splicing_project/splice-prediction/snakemake_workflows/Snakemake_Main/output/module1_qc_preproc_and_alignment/output/trimmomatic/76664_R2.fastq.gz, output/bwa/ref_genome/hg19.amb, output/bwa/ref_genome/hg19.ann, output/bwa/ref_genome/hg19.bwt, output/bwa/ref_genome/hg19.pac, output/bwa/ref_genome/hg19.sa
    output: bwa/mapped_custom2/76664.bam
    log: logs/bwa_mem_custom2/76664.log
    jobid: 0
    reason: Forced execution
    wildcards: sample=76664
    threads: 50
    resources: mem_mb=204800, disk_mb=15169, tmpdir=/tmp, cpus=50, time_min=360

python -c "import sys; print('.'.join(map(str, sys.version_info[:2])))"
Activating conda environment: .snakemake/conda/06e9e9e3769739946610da9d3cba085a
python /sc-scratch/sc-scratch-btg/olik_splicing_project/splice-prediction/snakemake_workflows/BWA_approach/.snakemake/scripts/tmphxhuz6z5.wrapper.py
Activating conda environment: .snakemake/conda/06e9e9e3769739946610da9d3cba085a
You have specified output format (`-O/--output-fmt`) in params.extra; this is automatically infered from output file extension.
Not cleaning up /sc-scratch/sc-scratch-btg/olik_splicing_project/splice-prediction/snakemake_workflows/BWA_approach/.snakemake/scripts/tmphxhuz6z5.wrapper.py

Minimal example

rule bwa_mem_custom1:
   input:
        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
        idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
    output:
        "mapped/{sample}.bam",
    log:
        "logs/bwa_mem/{sample}.log",
    params:
        extra="-O 4",
        sorting="samtools",  # Can be 'none', 'samtools' or 'picard'.
        sort_order="coordinate",  # Can be 'queryname' or 'coordinate'.
        sort_extra="",  # Extra args for samtools/picard.
    wrapper:
        "v1.17.3/bio/bwa/mem"

[github-actions]

This issue was marked as stale because it has been open for 6 months with no activity.

[fgvieira]

I think this has been fixed. Can you check?