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Add readOnlyInputs option for CharliecloudBuilder #3590

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merged 8 commits into from
Feb 2, 2023

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l-modolo
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This merge request is to add the readOnlyInputs option as discussed in the Charliecloud and shared cacheDir #3367 issue and following the Add readOnlyInputs option for CharliecloudBuilder #3477 merge request

With this modification:

  • the default readOnlyInputs value is false
  • if readOnlyInputs is true;
  • the -w option is removed from the command
  • the bound volumes are transformed to only mount the first folder of the path

For example, if I try to bind /home/user/workdir/ to /home/ the bound path will be /home to /home. By doing that, charliecloud doesn't try to mkdir -p /home/user/workdir/ within the read-only container, the external path is bound at the /home directory level so all the subfolders are accessible with the user rights. If one tries to bind / I added an expection.

Signed-off-by: Laurent Modolo laurent.modolo@ens-lyon.fr

Signed-off-by: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Signed-off-by: Laurent Modolo <laurent.modolo@ens-lyon.fr>
…r the readOnly parameter

Signed-off-by: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Signed-off-by: Laurent Modolo <laurent.modolo@ens-lyon.fr>
@pditommaso pditommaso merged commit 8ae001f into nextflow-io:master Feb 2, 2023
@pditommaso pditommaso added this to the 23.04.0 milestone Feb 21, 2023
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Included in version 23.02.0-edge

abhi18av pushed a commit to abhi18av/nextflow that referenced this pull request Oct 28, 2023
Signed-off-by: Laurent Modolo <laurent.modolo@ens-lyon.fr>
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2 participants