Bump Sambamba to 1.0.1

[scwatts]

• the Bioconda Sambamba packages >=0.8.1,<=1.0=h98b6b92_0 use an unoptimised binary, see:
  • Update Sambamba recipe to use release binary rather than test binary bioconda/bioconda-recipes#48071
  • Update sambamba to 1.0.1 bioconda/bioconda-recipes#48074
• I have observed a slowdown of ~8x when using the Bioconda Sambamba 1.0 package compared to the optimised binary for certain operations
• this PR updates the Sambamba modules to use the fixed Bioconda Sambamba package

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
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• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[scwatts]

Somewhat cryptic error:

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  
  sambamba 1.0.1
   by Artem Tarasov and Pjotr Prins (C) 2012-2023
      LDC 1.28.1 / DMD v2.098.1 / LLVM12.0.0 / bootstrap LDC - the LLVM D compiler (1.28.1)
  
  sambamba-markdup: /home/ubuntu/sambamba-pid16-markdup-srjw: Read-only file system

Trying to resolve by explicitly setting a temporary directory for Sambamba. I expect that changes to the command also result in a different checksum of the BAM, which will need to be updated if so.