Git default branch

[mirpedrol]

Closes #1688

If Git defaultBranch is set to dev or TEMPLATE nf-core commands that create a new pipeline repository fail with nice error message and the pipeline git repository is not initialised.

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[SamStudio8]

Hi @mirpedrol. I did not responsibly provide a complete suggestion in #1688. I wondered what would happen if the init.defaultBranch was not in the gitconfig. This code will need to catch configparser.NoSectionError and configparser.NoOptionError (or the base configparser.Error).

No [init] in .gitconfig

Traceback (most recent call last):
...
configparser.NoSectionError: No section: 'init'

[init] but no defaultBranch in .gitconfig

Traceback (most recent call last):
...
configparser.NoOptionError: No option 'defaultBranch' in section: 'init'

Error handling example

import git
import configparser

try:
    default_branch = git.config.GitConfigParser().get_value("init", "defaultBranch")
except configparser.Error:
    log.info("Could not read init.defaultBranch")
    default_branch = None

[codecov]

Codecov Report

Merging #1705 (9833007) into dev (3c22ebb) will increase coverage by 0.02%.
The diff coverage is 87.50%.

@@            Coverage Diff             @@
##              dev    #1705      +/-   ##
==========================================
+ Coverage   68.21%   68.23%   +0.02%     
==========================================
  Files          57       57              
  Lines        6736     6744       +8     
==========================================
+ Hits         4595     4602       +7     
- Misses       2141     2142       +1     

Impacted Files	Coverage Δ
nf_core/create.py	63.42% <87.50%> (+0.77%)	⬆️

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