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Currently, information in nextflow.config cannot be parsed properly.
This is because the type of text is not appropriate to parse using Python packages such as ConfigParser. Therefore, current approach is to get values and keys by reading strings line by line. (i. e. Example)

Suggestion

To have a package to read config files properly. For instance:

>> read_data = open(“nextflow.config”)

>> read_data.profiles
////
standard {includeConfig params.config}
docker { docker.enabled = true }
test { includeConfig 'conf/test.config' }
singularity {includeConfig 'conf/singularity.config'}
test_gatk_mode { includeConfig 'conf/test_gatk_mode_small.config' }
awsbatch { includeConfig 'conf/awsbatch.config' }
test_awsbatch { includeConfig 'conf/test_awsbatch.config' }
test_gatk_awsbatch { includeConfig 'conf/test_gatk_awsbatch.config' }
////

This improvement might facilitate:

• Linting
• Pipeline Automation
• Config Parsing

Description of desired behaviour

• The linter can detect if the name of the profile matches the basename of the respective config and report as a warning or error

profiles {
  should_fail { includeConfig 'conf/failing.config'}
  should_pass { includeConfig 'conf/should_pass.config' }
}

• The Github action can report as a reviewer in the PR

• The linting would provide a report similar to pytest where each screened profile status of the check should be

check: should_fail - FAILED ❌ 
check: should_pass - PASSED ✅ 

If even 1 profile check doesn’t pass, then the ci test, should fail

• Add option to ignore some profiles awsbatch etc

References:

• pytest output
• codecov output

https://github.com/lifebit-ai/metagwas-nf/pull/31/commits/8377ade86f6380013d2b63713507ecc0951bed05#diff-0b5ca119d2be595aa307d34512d9679e49186307ef94201e4b3dfa079aa89938R799