Module import

[ewels]

Continuation of #579 so that more people can contribute.

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Proof-of-concept pull request for building a simplistic import system tools from nf-core/modules into pipelines.

See nf-core/modules#8 for (extensive) discussion.

Current functionality:

$ nf-core modules --help


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    nf-core/tools version 1.10.dev0

Usage: nf-core modules [OPTIONS] COMMAND [ARGS]...

  Manage DSL 2 module imports

Options:
  -r, --repository TEXT  GitHub repository name.
  -b, --branch TEXT      The git branch to use.
  --help                 Show this message and exit.

Commands:
  list     List available tools
  install  Install a DSL2 module
  update   Update one or all DSL2 modules
  remove   Remove a DSL2 module
  check    Check that imported module code has not been modified
  fix      Replace imported module code with a freshly downloaded copy

$ nf-core modules list

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    nf-core/tools version 1.10.dev0


INFO: Tools available from nf-core/modules (master):

bwa
cutadapt
fastqc
gatk
htslib
samtools
trim_galore

$  nf-core modules install fastqc

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$ ls modules/tools/fastqc/
main.nf   meta.yml  test/

[codecov]

Codecov Report

Merging #615 into dev will increase coverage by 0.19%.
The diff coverage is 80.25%.

@@            Coverage Diff             @@
##              dev     #615      +/-   ##
==========================================
+ Coverage   76.49%   76.69%   +0.19%     
==========================================
  Files          12       13       +1     
  Lines        2463     2617     +154     
==========================================
+ Hits         1884     2007     +123     
- Misses        579      610      +31     

Impacted Files	Coverage Δ
nf_core/__main__.py	65.16% <66.10%> (-0.27%)	⬇️
nf_core/modules.py	88.77% <88.77%> (ø)

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[drpatelh]

All LGTM! Happy for a merge so we can get testing with it all 👍