Code

nf-schema support#3116

Code

Merged

nvnieuwk merged 69 commits intonf-core:devnf-core/tools:devfrom nvnieuwk:feat/linting-nf-schemanvnieuwk/tools:feat/linting-nf-schemaCopy head branch name to clipboardAug 27, 2024

+1,083-972

Commits

Commits on Aug 14, 2024

• add schema checking for draft 2020-12

  nvnieuwk

  committed
  a754fe0

• update validate schema

  nvnieuwk

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  464f16e

• update more code to support draft 2020-12

  nvnieuwk

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  6658449

• fix draft 7 schema using http

  nvnieuwk

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  6ecde20

• ruff

  nvnieuwk

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  36fad24

• fix tests + add draft 2020-12 as default draft

  nvnieuwk

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  6777694

• fix typo

  nvnieuwk

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  0dfd15d

• ruff

  nvnieuwk

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  7f29f37

• add checks for nf-validation and nf-schema plugin config

  nvnieuwk

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  730c677

• linting fully works now!

  nvnieuwk

  committed
  7fbbff7

Commits on Aug 19, 2024

• Merge branch 'dev' into feat/linting-nf-schema

  nvnieuwk

  authored
  59e2eb0

• warning for nf-validation

  nvnieuwk

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  0838d6b

• Merge branch 'feat/linting-nf-schema' of github.com:nvnieuwk/tools into feat/linting-nf-schema

  nvnieuwk

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  ba329fa

• fetch plugin on schema filename setting

  nvnieuwk

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  8559c2d

• add a check for defs usage instead of $defs

  nvnieuwk

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  0296f7d

• change all definitions to self.defs_notation

  nvnieuwk

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  0b8d04f

• migrate template part 1

  nvnieuwk

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  5443813

Commits on Aug 20, 2024

• some small updates for the new release

  nvnieuwk

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  5519c83

• some more small updates to the template

  nvnieuwk

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  171640b

• update handling of ignored parameters

  nvnieuwk

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  249b3da

• update validation plugin fetching

  nvnieuwk

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  af34d07

Commits on Aug 21, 2024

• update plugin linting

  nvnieuwk

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  e6381b7

• ignore genomes for now

  nvnieuwk

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  e66a732

• improve config linting for validation even more

  nvnieuwk

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  b6ae8d0

• check plugin includes in pipeline

  nvnieuwk

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  1be1737

Commits on Aug 22, 2024

• make nf-schema optional in the template

  nvnieuwk

  committed
  2f1a442

• Merge branch 'dev' into feat/linting-nf-schema

  nvnieuwk

  authored
  72aa81f

• small fixes for template without nf-schema

  nvnieuwk

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  364b54b

• bump nextflow version

  nvnieuwk

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  4e63138

• update changelog

  nvnieuwk

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  11efc55

• fix ruff linting

  nvnieuwk

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  47c3fe3

• add a plugin includes test

  nvnieuwk

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  09bfca2

Commits on Aug 23, 2024

• update review comments

  nvnieuwk

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  44dbbf7

• remove duplicate code

  nvnieuwk

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  ea51814

Commits on Aug 26, 2024

• update nf-schema subwf

  nvnieuwk

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  b85ea4d

• Merge branch 'dev' into feat/linting-nf-schema

  nvnieuwk

  authored
  c538cfd

• fix some issues

  nvnieuwk

  committed
  0fb97db

• fix linting utils_nfschema_plugin

  nvnieuwk

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  7dee447

• update utils subwfs

  nvnieuwk

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  6d01b0f

Commits on Aug 27, 2024

• fix some linting issues

  nvnieuwk

  committed
  a7dcdd7

• Merge branch 'dev' into feat/linting-nf-schema

  nvnieuwk

  authored
  a77f5a1

• ruff

  nvnieuwk

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  fcdf65b

• add linting doc for plugin_includes

  nvnieuwk

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  56150dc

• readd file exists check

  nvnieuwk

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  5a29c4e

• fix launch command

  nvnieuwk

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  18738ef

• fix schema tests

  nvnieuwk

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  ebf6a27

• ruff

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  04fabe5

• readd file exists check

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  0649a75

• fix lint test

  nvnieuwk

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  9fd9869

• update textual snapshots

  mirpedrol

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  6cccc1e

• skip linting before and after Text params for custom pipelines

  mirpedrol

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  2ccbdd9

• typo

  mirpedrol

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  ed01eba

• Update nf_core/pipeline-template/nextflow.config

  Show description for 1b597f1
  

  nvnieuwk

  and

  mirpedrol

  authored
  1b597f1

• Update nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

  Show description for 93cc41b
  

  nvnieuwk

  and

  mirpedrol

  authored
  93cc41b

• Update nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

  Show description for 6e358f3
  

  nvnieuwk

  and

  mirpedrol

  authored
  6e358f3

• Update nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf

  Show description for dbe9318
  

  nvnieuwk

  and

  mirpedrol

  authored
  dbe9318

• Update nf_core/pipelines/create/templatefeatures.yml

  Show description for 4025b54
  

  nvnieuwk

  and

  mirpedrol

  authored
  4025b54

• Update tests/pipelines/lint/test_plugin_includes.py

  Show description for 679de82
  

  nvnieuwk

  and

  mirpedrol

  authored
  679de82

• review suggestions

  nvnieuwk

  committed
  3ac1bd8

• use latest version of utils_nextflow_pipeline

  nvnieuwk

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  d4266c0

• make help params snake_case

  nvnieuwk

  committed
  bc20099

• Update nf_core/pipelines/create/templatefeatures.yml

  Show description for 829d594
  

  nvnieuwk

  and

  mashehu

  authored
  829d594

• Update nf_core/pipelines/lint/plugin_includes.py

  Show description for 1ff7cbc
  

  nvnieuwk

  and

  mashehu

  authored
  1ff7cbc

• apply review suggestions

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  committed
  aed9460

• Merge branch 'feat/linting-nf-schema' of github.com:nvnieuwk/tools into feat/linting-nf-schema

  nvnieuwk

  committed
  7612e66

• update utils_nextflow_pipeline commit messages

  nvnieuwk

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  4407901

• update ignoring of help params

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  330e43c

• update file exists docstring

  nvnieuwk

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  3600db7

• update snapshot

  nvnieuwk

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  e816faf