Module import

[ewels]

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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    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

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

  Manage DSL 2 module imports

Options:
  --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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    |\ | |__  __ /  ` /  \ |__) |__         }  {
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                                          `._,._,'


INFO: Tools available from nf-core/modules:

bwa
fastqc
gatk
htslib
samtools
trim_galore

$  nf-core modules install fastqc

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    |\ | |__  __ /  ` /  \ |__) |__         }  {
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                                          `._,._,'

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

[ewels]

Merging into module-import branch so that others can work on the code..

[codecov]

Codecov Report

Merging #579 into module-import will decrease coverage by 2.66%.
The diff coverage is 0.00%.

@@                Coverage Diff                @@
##           module-import     #579      +/-   ##
=================================================
- Coverage          66.55%   63.89%   -2.67%     
=================================================
  Files                 11       12       +1     
  Lines               1848     1925      +77     
=================================================
  Hits                1230     1230              
- Misses               618      695      +77     

Impacted Files	Coverage Δ
nf_core/modules.py	0.00% <0.00%> (ø)

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