Creating a new module (seq2HLA) fails ungracefully
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bug
- Dominant language
- Python
- Stars
- 322
- Forks
- 255
- Avg merge
- 2d 3h
- Merged PRs (30d)
- 5
Description
Description of the bug
When creating a new module in the modules repo with 3.4.0dev, the creation itself appears to work, but still the command fails ungracefully:
Command used and terminal output
> nf-core modules create
nf-core/tools version 3.4.0.dev0 - https://nf-co.re
INFO Repository type: modules
INFO Press enter to use default values (shown in brackets) or type your own responses. ctrl+click underlined text to open links.
INFO Using Bioconda package: 'bioconda::seq2hla=2.3'
INFO Using Docker container: 'biocontainers/seq2hla:2.3--hdfd78af_1'
INFO Using Singularity container: 'https://depot.galaxyproject.org/singularity/seq2hla:2.3--hdfd78af_1'
INFO Found bio.tools information for 'seq2hla'
INFO Found bio.tools ID: 'biotools:seq2hla'
GitHub Username: (@author): @FriederikeHanssen
INFO Provide an appropriate resource label for the process, taken from the nf-core pipeline template.
For example: process_single, process_low, process_medium, process_high, process_long, process_high_memory
? Process resource label: process_single
INFO Where applicable all sample-specific information e.g. 'id', 'single_end', 'read_group' MUST be provided as an input via a Groovy Map called
'meta'. This information may not be required in some instances, for example indexing reference genome files.
Will the module require a meta map of sample information? [y/n] (y): y
INFO Created component template: 'seq2hla'
CRITICAL Can't format ['modules/nf-core/seq2hla/main.nf', 'modules/nf-core/seq2hla/meta.yml', 'modules/nf-core/seq2hla/environment.yml',
'modules/nf-core/seq2hla/tests/main.nf.test'] because it has a syntax error.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-prettier.
[INFO] Initializing environment for https://github.com/pre-commit/mirrors-prettier:prettier@2.7.1.
[INFO] Installing environment for https://github.com/pre-commit/mirrors-prettier.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
prettier.................................................................Failed
- hook id: prettier
- exit code: 2
modules/nf-core/seq2hla/meta.yml: SyntaxError: Sequence items must not have preceding content on the same line (26:13)
24 | output:
25 | # TODO nf-core: Update the information obtained from bio.tools and make sure that it is correct
> 26 | versions: -
| ^
> 27 | versions.yml:
| ^^^^^^^^^^^^^^^^^
> 28 | type: file
| ^^^^^^^^^^^^^^^^^
> 29 | description: File containing software versions
| ^^^^^^^^^^^^^^^^^
> 30 | pattern: versions.yml
| ^^^^^^^^^^^^^^^^^
> 31 | ontologies:
| ^^^^^^^^^^^^^^^^^
> 32 | - edam: http://edamontology.org/format_3750 # YAML
| ^^^^^^^^^^^^^^^^^
> 33 | authors:
| ^
34 | - "@FriederikeHanssen"
35 | maintainers:
36 | - "@FriederikeHanssen"
INFO Created following files:
modules/nf-core/seq2hla/main.nf
modules/nf-core/seq2hla/meta.yml
modules/nf-core/seq2hla/environment.yml
modules/nf-core/seq2hla/tests/main.nf.test
System information
tools version: 3.4.0.dev0
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the failure with nf-core modules create using tools version 3.4.0.dev0, then inspect the generated modules/nf-core/seq2hla/meta.yml around the versions output. Run the reported Prettier hook against the created files; done means module creation completes without the YAML syntax error and the generated files are formatted successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100