Support running nextflow script in cygwin #6367
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Support running in cygwin by translating cygwin-style paths (starting with /cygrdrive/) to windows-style paths. Signed-off-by: Mark Woon <[email protected]>
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pditommaso
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Sep 2, 2025
nextflow
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| NXF_VER=${NXF_VER:-'25.07.0-edge'} | ||
| NXF_ORG=${NXF_ORG:-'nextflow-io'} | ||
| NXF_HOME=${NXF_HOME:-$HOME/.nextflow} | ||
| NXF_HOME=${NXF_HOME:-$home/.nextflow} |
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Why using home instead of HOME? think this will break default launcher
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If you look at line 19 of my commit, you'll see that home is a local variable.
The whole point is to rewrite cygwin mounts as windows mounts so that the script works.
Would you prefer if I named it something else? Maybe normalized_home?
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I see. indeed it would be preferable to use a different name. what about using NXF_HOME (if not defined yet)?
avoid local variable "home" per request Signed-off-by: Mark Woon <[email protected]>
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How about this? |
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Support running in cygwin by translating cygwin-style paths (starting with /cygrdrive/) to windows-style paths.