Fix for Azure certificates compatibility

[adamrtalbot]

When running a CentOS container on a Debian based virtual machine on Azure (default), an error was thrown while mounting the certificates. This was because we tried to add them by default. This PR changes the behaviour so this no longer happens. A user can still renable these options using the container.runOptions as per any other Docker runner.

Fixes #4828

Signed-off-by: Adam Talbot 12817534+adamrtalbot@users.noreply.github.com

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[adamrtalbot]

Steps to show it works:

main.nf:

process HELLO {
    container "docker.io/redhat/ubi8:8.9"

    output:
        stdout
    
    script:
    """
    echo "Hello, World!"
    """
}

workflow {
    HELLO()
}

Config:

process {
    executor = 'azurebatch'
}

azure {
    storage {
        accountName = "$AZURE_STORAGE_ACCOUNT_NAME"
        accountKey = "$AZURE_STORAGE_ACCOUNT_KEY"
    }
    batch {
        location = "$AZURE_LOCATION"
        accountName = "$AZURE_BATCH_ACCOUNT_NAME"
        accountKey = "$AZURE_BATCH_ACCOUNT_KEY"
        autoPoolMode = true
        deletePoolsOnCompletion = true
        deleteTasksOnCompletion = false
    }
}

Command:

nextflow-dev run . -c nextflow.config

Output:

> nextflow-dev run . -c nextflow.config -w az://scidev-useast/
N E X T F L O W  ~  version 24.02.0-edge
Launching `./main.nf` [silly_waddington] DSL2 - revision: 11eb8eab2e
[5c/75b8a6] Submitted process > HELLO

From Batch Explorer (note no container run options):

[adamrtalbot]

Shoot. Integration tests fail:

Launching `./test-complexpaths.nf` [thirsty_bohr] DSL2 - revision: 44828720b8
[47/0ffbb5] Submitted process > foo
ERROR ~ Error executing process > 'foo'

Caused by:
  Missing output file(s) `*.fa` expected by process `foo`

Command executed:

  echo A > hello.txt
  echo B > sample.zip 
  echo C > sample.html
  echo D > 01_A\(R1\).fastq
  echo E > 01_A\(R2\).fastq
  echo F > sample_\(1\ 2\).vcf
  echo 1 > f1.fa
  echo 2 > f2.fa
  echo 3 > f3.fa
  mkdir .alpha
  echo "Hello world!" > .alpha/hello.txt

Command exit status:
  0

Command output:
  (empty)

[pditommaso]

[pditommaso]

This doesn't look nice

[adamrtalbot]

It also doesn't work.

[adamrtalbot]

Removed.