https://nf-co.re logo
Join Slack
Powered by
I get the following error when running `nf-core pi...
# tools
n
I get the following error when running `nf-core pipelines lint`: 
ERROR    Could not find the org_path in the configuration file: .nf-core.yml
. While this is in my .nf-core.yml: 
org_path: nf-cmgg
, what am I doing wrong here?
m
can you show your full .nf-core.yml?
n
Copy code
bump_version:
lint:
  actions_ci: false
  files_exist:
    - CODE_OF_CONDUCT.md
    - assets/nf-core-smallvariants_logo_light.png
    - docs/images/nf-core-smallvariants_logo_light.png
    - docs/images/nf-core-smallvariants_logo_dark.png
    - .github/ISSUE_TEMPLATE/config.yml
    - .github/workflows/awstest.yml
    - .github/workflows/awsfulltest.yml
    - .github/workflows/template_version_comment.yml
    - docs/README.md
    - tests/default.nf.test
  files_unchanged:
    - .github/CONTRIBUTING.md
    - .github/PULL_REQUEST_TEMPLATE.md
    - .github/workflows/branch.yml
    - .github/workflows/linting_comment.yml
    - .github/workflows/linting.yml
    - CODE_OF_CONDUCT.md
    - .github/ISSUE_TEMPLATE/bug_report.yml
    - .prettierignore
    - LICENSE
  multiqc_config:
    - report_comment
  nextflow_config:
    - custom_config
    - manifest.name
    - manifest.homePage
    - validation.help.afterText
    - validation.summary.afterText
nf_core_version: 3.4.1
repository_type: pipeline
org_path: nf-cmgg
template:
  author: nvnieuwk
  description: A nextflow pipeline for calling and annotating small smallvariants
    variants from short DNA reads for WES and WGS data
  force: false
  is_nfcore: false
  name: smallvariants
  org: nf-cmgg
  outdir: .
  skip_features:
    - fastqc
    - is_nfcore
  version: 1.11.1dev
m
can you run 
nf-core --verbose p lint
?
n
Copy code
DEBUG    sys.platform='linux', git_executable='git'                                                                                                                                                                                            util.py:494
DEBUG    Popen(['git', 'cat-file', '--batch-check'], cwd=/home/nvnieuwk/Documents/nf-cmgg/smallvariants, stdin=<valid stream>, shell=False, universal_newlines=False)                                                                          cmd.py:1270
DEBUG    Got '.' as path                                                                                                                                                                                                                      utils.py:349
DEBUG    Found a config cache, loading: /home/nvnieuwk/.nextflow/nf-core/wf-config-cache-5abe9819e64232cb2bc6c8b98.json                                                                                                                       utils.py:383
DEBUG    Using config file: .nf-core.yml                                                                                                                                                                                                     utils.py:1481
DEBUG    Got '.' as path                                                                                                                                                                                                                      utils.py:349
DEBUG    Found a config cache, loading: /home/nvnieuwk/.nextflow/nf-core/wf-config-cache-5abe9819e64232cb2bc6c8b98.json                                                                                                                       utils.py:383
DEBUG    sys.platform='linux', git_executable='git'                                                                                                                                                                                            util.py:494
DEBUG    Popen(['git', 'version'], cwd=/home/nvnieuwk/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                       cmd.py:1270
DEBUG    Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/nvnieuwk/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True)                                                                      cmd.py:1270
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/home/nvnieuwk/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                            cmd.py:1270
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/home/nvnieuwk/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                        cmd.py:1270
DEBUG    Got '/home/nvnieuwk/.config/nfcore/nf-core/modules' as path                                                                                                                                                                          utils.py:349
DEBUG    Found a config cache, loading: /home/nvnieuwk/.nextflow/nf-core/wf-config-cache-9f4bce35ba6f9f759cbf54fa7.json                                                                                                                       utils.py:383
DEBUG    Using config file: /home/nvnieuwk/.config/nfcore/nf-core/modules/.nf-core.yml                                                                                                                                                       utils.py:1481
ERROR    Could not find the org_path in the configuration file: .nf-core.yml
seems like the nf-core yaml location is wrong
m
or that there is a second wrong one
inception 1
n
hmmm okay it seems to use the one from the cached version of the modules repo, I'll try removing it
m
weird
n
removing the cached versions seems to fix it 😛
thanks for rubber ducking 😉
3 Views
Open in Slack
PreviousNext
Powered by