`nf-core pipelines lint --release`
getting
```INFO...
# lintings
Sateesh_Peri
09/27/2024, 1:59 PMnf-core pipelines lint --release Copy code
INFO Testing pipeline: .
INFO Including --release mode tests
Running lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 of 24 » files_existINFO Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema.
Running lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7 of 24 » pipeline_todosERROR [✗] Pipeline schema does not follow nf-core specs:
Schema is using the wrong draft: <http://json-schema.org/draft-07/schema>, should be <https://json-schema.org/draft/2020-12/schema>
Running lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12 of 24 » schema_paramsERROR [✗] Pipeline schema does not follow nf-core specs:
Schema is using the wrong draft: <http://json-schema.org/draft-07/schema>, should be <https://json-schema.org/draft/2020-12/schema>
CRITICAL Critical error: [✗] Pipeline schema does not follow nf-core specs:
Schema is using the wrong draft: <http://json-schema.org/draft-07/schema>, should be <https://json-schema.org/draft/2020-12/schema>
INFO Stopping tests...m
mashehu
09/27/2024, 2:01 PMnf-schema, uses a newer schema draft. just replace the value (and
definitions$defss
Sateesh_Peri
09/27/2024, 2:05 PMcould you share the migration guide plz ?
m
mashehu
09/27/2024, 2:06 PMgratitude thank you 1
s
Sateesh_Peri
09/28/2024, 1:06 PMany pipelines that finished the migration ? im seeing rnaseq, sarek, nascent are still on the old one
Sateesh_Peri
09/28/2024, 3:43 PMI tried following the guide now see more errors
Copy code
INFO Testing pipeline: .
INFO Including --release mode tests
Running lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 of 24 » files_existINFO Could not find nf-schema or nf-validation in the pipeline config. Defaulting to nf-schema notation for the JSON schema.
╭─ [?] 4 Pipeline Tests Ignored ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File is ignored: lib/nfcore_external_java_deps.jar │
│ files_exist: File is ignored: conf/modules.config │
│ actions_ci: actions_ci │
│ modules_config: modules_config │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 2 Pipeline Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_exist: File not found: conf/igenomes_ignored.config │
│ nfcore_yml: nf-core version in .nf-core.yml is not set to the latest version. Should be 3.0.0.dev0 but was 2.14.1 │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 11 Pipeline Tests Failed ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ │
│ nextflow_config: Plugin 'nf-amazon' does not have a pinned version │
│ nextflow_config: Config variable (incorrectly) found: params.max_cpus │
│ nextflow_config: Config variable (incorrectly) found: params.max_memory │
│ nextflow_config: Config variable (incorrectly) found: params.max_time │
│ files_unchanged: .github/CONTRIBUTING.md does not match the template │
│ files_unchanged: .github/PULL_REQUEST_TEMPLATE.md does not match the template │
│ files_unchanged: .github/workflows/linting_comment.yml does not match the template │
│ files_unchanged: .github/workflows/linting.yml does not match the template │
│ files_unchanged: .prettierignore does not match the template │
│ actions_awsfulltest: .github/workflows/awsfulltest.yml is not triggered correctly │
│ schema_params: Param validationSchemaIgnoreParams from nextflow config not found in nextflow_schema.json │
│ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 1 Subworkflow Test Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ ╷ ╷ │
│ Subworkflow name │ File path │ Test message │
│╶───────────────────────────┼────────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ utils_nfvalidation_plugin │ subworkflows/nf-core/utils_nfvalidation_plugin/main.nf │ Local copy of subworkflow does not match remote │
│ ╵ ╵ │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 294 Tests Passed │
│ [?] 4 Tests Ignored │
│ [!] 2 Test Warnings │
│ [✗] 12 Tests Failed │
╰───────────────────────╯
Tip: Some of these linting errors can automatically be resolved with the following command:
nf-core pipelines lint --dir . --fix files_unchanged
INFO Reminder: Lint tests were run in --release mode.p
Phil Ewels
09/28/2024, 6:51 PM@Sateesh_Peri are you running with tools dev version? Or latest stable?
Phil Ewels
09/28/2024, 6:52 PMI was thinking it would be easiest to use latest stable and get this out before v3 drops
✅ 1