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Respect NXF_HOME #798

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ewels opened this issue Nov 26, 2020 · 0 comments
Closed

Respect NXF_HOME #798

ewels opened this issue Nov 26, 2020 · 0 comments
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bug Something isn't working command line tools Anything to do with the cli interfaces

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@ewels
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ewels commented Nov 26, 2020

If you set the environment variable NXF_HOME, then some of the nf-core/tools features such as nf-core list do not work properly.

Here is the relevant code block in this example:

tools/nf_core/list.py

Lines 129 to 132 in b67fd2a

if len(os.environ.get("NXF_ASSETS", "")) > 0:
nextflow_wfdir = os.environ.get("NXF_ASSETS")
else:
nextflow_wfdir = os.path.join(os.getenv("HOME"), ".nextflow", "assets")

Need to also check for NXF_HOME as well as NXF_ASSETS (and any others?) and use that if set, before finally defaulting to the home directory path. Should also check the codebase for any other places where the same thing happens.

@ewels ewels added bug Something isn't working command line tools Anything to do with the cli interfaces labels Nov 26, 2020
ewels added a commit to ewels/nf-core-tools that referenced this issue Nov 26, 2020
@ewels ewels closed this as completed Nov 27, 2020
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Labels
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