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Remove nf-core modules check #878

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Merged
drpatelh merged 29 commits into from
Mar 15, 2021
Merged

Remove nf-core modules check #878

drpatelh merged 29 commits into from
Mar 15, 2021
+270 −293

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@ewels ewels commented Mar 15, 2021 •
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@ewels ewels added the WIP Work in progress label Mar 15, 2021
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codecov bot commented Mar 15, 2021 •
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Codecov Report

Merging #878 (494477f) into dev (bedbe53) will decrease coverage by 0.04%.
The diff coverage is 61.46%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #878      +/-   ##
==========================================
- Coverage   71.13%   71.08%   -0.05%     
==========================================
  Files          33       33              
  Lines        3596     3604       +8     
==========================================
+ Hits         2558     2562       +4     
- Misses       1038     1042       +4
Impacted Files Coverage Δ
nf_core/list.py 82.23% <ø> (-0.08%) ⬇️
nf_core/modules/test_yml_builder.py 16.98% <0.00%> (-0.11%) ⬇️
nf_core/__main__.py 61.53% <39.28%> (-1.09%) ⬇️
nf_core/modules/create.py 63.75% <73.33%> (+1.75%) ⬆️
nf_core/modules/pipeline_modules.py 86.15% <74.19%> (-2.55%) ⬇️

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drpatelh
drpatelh reviewed Mar 15, 2021
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drpatelh commented Mar 15, 2021

Do we remove the update command too?

@ewels ewels marked this pull request as ready for review March 15, 2021 14:09
@ewels ewels added command line tools Anything to do with the cli interfaces DSL2 and removed WIP Work in progress labels Mar 15, 2021
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ewels commented Mar 15, 2021

Made an awesome fuzzy-finder interface when installing modules which I kind of love:

Mar-15-2021 15-12-09

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ewels commented Mar 15, 2021

Do we remove the update command too?

Yup, it's gone from the command line interface. I commented it out and left the stub as we do intend to put that in at a later date (I completely deleted check as that's part of lint).

@ewels ewels force-pushed the modules-cleanup branch from 0e91b49 to 0d96227 Compare March 15, 2021 15:31
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drpatelh commented Mar 15, 2021

As mentioned on Slack we need to change where these modules are installed locally:

tools/nf_core/modules/create.py

Line 51 in d0b7daf

'directory/modules/local/process' dir called <tool_subtool.nf>

Need to change this install path to directory/modules/local/ i.e. without the process - based on recent module restructuring in #viralrecon

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ewels commented Mar 15, 2021

Dropped process dir in 336de7d 👍🏻

ewels and others added 3 commits March 15, 2021 17:39
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drpatelh approved these changes Mar 15, 2021
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Pleasure as always Sir! 💥

@drpatelh drpatelh merged commit a688788 into nf-core:dev Mar 15, 2021
@ewels ewels deleted the modules-cleanup branch March 15, 2021 22:05
@ewels ewels mentioned this pull request Mar 15, 2021
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