Cryptic error by lint when file in modules/local has no process definition

[d4straub]

Is your feature request related to a problem? Please describe

nf-core lint reports a cryptic error when there is no process name in a file in modules/local.

Describe the solution you'd like

Ideally, printing the module/file that is failing.

Describe alternatives you've considered

Alternatively, printing that one of the files in modules/local lacks a process definition.

Additional context

nf-core lint error message:

Run nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
shell: /usr/bin/bash -e {0}
env:
pythonLocation: /opt/hostedtoolcache/Python/3.6.14/x64
GITHUB_COMMENTS_URL:
GITHUB_TOKEN: ***
GITHUB_PR_COMMIT:
,--./,-.
___ __ __ __ ___ /,-..--~
|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,.,'
nf-core/tools version 2.0.1
INFO Testing pipeline: /home/runner/work/ampliseq/ampliseq init.py:212
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /opt/hostedtoolcache/Python/3.6.14/x64/bin/nf-core:8 in │
│ │
│ 7 │ sys.argv[0] = re.sub(r'(-script.pyw|.exe)?$', '', sys.argv[0]) │
│ ❱ 8 │ sys.exit(run_nf_core()) │
│ 9 │
│ │
[....]
│ │
│ /opt/hostedtoolcache/Python/3.6.14/x64/lib/python3.6/site-packages/nf_core/m │
│ odules/lint/main_nf.py:151 in check_process_section │
│ │
│ 150 │ # Process name should be all capital letters │
│ ❱ 151 │ self.process_name = lines[0].split()[1] │
│ 152 │ if all([x.upper() for x in self.process_name]): │
╰──────────────────────────────────────────────────────────────────────────────╯
IndexError: list index out of range
Error: Process completed with exit code 1.

Can be also found in https://github.com/d4straub/ampliseq/runs/3171484455

The actual problem was that one file in modules/local was actually not describing a process and was clearly in the wrong folder, see here.

[chasemc]

Had an empty file in modules/local, same error