Inconsistent behaviour when using modules info in a local clone

[awgymer]

Description of the bug

Not entirely sure if this is a bug, or misuse of the tools.

When running nf-core modules info and trying to get the information of the module in a local clone the expected output is correct if the module is <tool> but comes from the remote if the module is <tool>/<subtool>

As you can see below, mosdepth returns the info from the "local" repo clone but samtools/merge returns the info from the actual remote.

Command used and terminal output

❯ nf-core -v modules info

Pulling from 'nf-core/modules' (https://github.com/nf-core/modules.git) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Waiting for responseDEBUG    Popen(['git', 'version'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                                             cmd.py:870
DEBUG    Popen(['git', 'fetch', '-v', '--progress', 'origin'], cwd=<path>, universal_newlines=True, shell=None, istream=None)                  cmd.py:870
DEBUG    Popen(['git', 'checkout', 'master'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                                  cmd.py:870
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                              cmd.py:870
DEBUG    Found modules repo: .                                                                                                                                                            info.py:69
DEBUG    Using selector: KqueueSelector                                                                                                                                        selector_events.py:59
? Is the module locally installed? Yes
? Please select a module samtools/merge
DEBUG    Module 'samtools/merge' meta.yml not found locally                                                                                                                              info.py:165
DEBUG    Popen(['git', 'checkout', 'master'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                                  cmd.py:870
DEBUG    Popen(['git', 'checkout', 'master'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                                  cmd.py:870
╭─ Module: samtools/merge  ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ 🌐 Repository: https://github.com/nf-core/modules.git                                                                                                                                            │
│ 🔧 Tools: samtools                                                                                                                                                                               │
│ 📖 Description: Merge BAM or CRAM file                                                                                                                                                           │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

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nf-core -v modules info

Pulling from 'nf-core/modules' (https://github.com/nf-core/modules.git) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Waiting for responseDEBUG    Popen(['git', 'version'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                                             cmd.py:870
DEBUG    Popen(['git', 'fetch', '-v', '--progress', 'origin'], cwd=<path>, universal_newlines=True, shell=None, istream=None)                  cmd.py:870
DEBUG    Popen(['git', 'checkout', 'master'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                                  cmd.py:870
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=<path>, universal_newlines=False, shell=None, istream=None)                              cmd.py:870
DEBUG    Found modules repo: .                                                                                                                                                            info.py:69
DEBUG    Using selector: KqueueSelector                                                                                                                                        selector_events.py:59
? Is the module locally installed? Yes
? Please select a module mosdepth
DEBUG    Found local file: ./modules/mosdepth/meta.yml                                                                                                                                   info.py:161
╭─ Module: mosdepth  ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ Location: ./modules/mosdepth                                                                                                                                                                     │
│ 🔧 Tools: mosdepth                                                                                                                                                                               │
│ 📖 Description: Calculates genome-wide sequencing coverage.                                                                                                                                      │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

System information

nf-core/tools version 2.5.dev0 MacOS Python 3.9.7