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Make Nextflow compatible with NixOS (or other systems without /bin/bash) #5432

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Commits on Oct 22, 2024

  1. Allow Nextflow to be used on (host) systems without /bin/bash

    On systems without /bin/bash (e.g. NixOS), invoking tasks may fail because
    of some hard-coded references to /bin/bash. Those references are either fine
    (because the task runs in a container where /bin/bash *is* available),
    don't matter (because the shebang is ignored) or cause failure (because
    /bin/bash cannot be invoked). This commit adapts Nextflow for the last
    scenario. Instead of invoking `/bin/bash`, the actually available bash
    executable is called.
    
    Signed-off-by: Rolf Schröder <[email protected]>
    rollf committed Oct 22, 2024
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Commits on Oct 25, 2024

  1. Use /usr/bin/env -S bash instead of which bash.

    This is more portable. This commit also makes sure that `-ue[x]` is not
    used during trace.
    
    Signed-off-by: Rolf Schröder <[email protected]>
    rollf committed Oct 25, 2024
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  2. Use initial boolean variable instead of a derived one.

    Signed-off-by: Rolf Schröder <[email protected]>
    rollf committed Oct 25, 2024
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  3. Do not invoke /usr/bin/env -S bash when tracing.

    Signed-off-by: Rolf Schröder <[email protected]>
    rollf committed Oct 25, 2024
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  4. Always consider the (non-)container context when deciding which bash

    to use.
    
    Signed-off-by: Rolf Schröder <[email protected]>
    rollf committed Oct 25, 2024
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