updated pre-commit configs

.editorconfig

@@ -8,8 +8,8 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
-indent_size = 2
+[*.{json,md,yml,yaml,html,css,scss,js,cff}]
+indent_size = unset
 
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
@@ -22,3 +22,4 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -2,52 +2,52 @@ name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-- type: textarea
-  id: description
-  attributes:
-    label: Description of the bug
-    description: A clear and concise description of what the bug is.
-  validations:
-    required: true
-- type: textarea
-  id: command_used
-  attributes:
-    label: Command used and terminal output
-    description: Steps to reproduce the behaviour. Please paste the command you used
-      to launch the pipeline and the output from your terminal.
-    render: console
-    placeholder: '$ nextflow run ...
-
-
-      Some output where something broke
-
-      '
-- type: textarea
-  id: files
-  attributes:
-    label: Relevant files
-    description: 'Please drag and drop the relevant files here. Create a `.zip` archive
-      if the extension is not allowed.
-
-      Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
-      in the directory where you launched the pipeline)_ as well as custom Nextflow
-      configuration files.
-
-      '
-- type: textarea
-  id: system
-  attributes:
-    label: System information
-    description: '* Nextflow version _(eg. 22.10.1)_
-
-      * Hardware _(eg. HPC, Desktop, Cloud)_
-
-      * Executor _(eg. slurm, local, awsbatch)_
-
-      * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
-
-      * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-
-      * Version of mk-kondo/mikrokondo _(eg. 1.1, 1.5, 1.8.2)_
-
-      '
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used
+        to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: "$ nextflow run ...
+
+
+        Some output where something broke
+
+        "
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: "Please drag and drop the relevant files here. Create a `.zip` archive
+        if the extension is not allowed.
+
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file
+        in the directory where you launched the pipeline)_ as well as custom Nextflow
+        configuration files.
+
+        "
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: "* Nextflow version _(eg. 22.10.1)_
+
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+
+        * Executor _(eg. slurm, local, awsbatch)_
+
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+
+        * Version of mk-kondo/mikrokondo _(eg. 1.1, 1.5, 1.8.2)_
+
+        "

.github/workflows/ci.yml

@@ -60,4 +60,3 @@ jobs:
       - name: Nextflow run with test profile
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-

.github/workflows/spellcheck.yml

@@ -1,4 +1,3 @@
-
 name: Spellcheck Action
 
 on:
@@ -12,20 +11,19 @@ jobs:
     name: Spellcheck
     runs-on: ubuntu-latest
     steps:
+      # The checkout step
+      - uses: actions/checkout@v4
 
-    # The checkout step
-    - uses: actions/checkout@v4
-
-    - uses: rojopolis/spellcheck-github-actions@v0
-      name: Spellcheck
-      with:
-        source_files: README.md CHANGELOG.md nextflow_schema.json assets/schema_input.json
-        task_name: Markdown
-        output_file: spellcheck-output.txt
+      - uses: rojopolis/spellcheck-github-actions@v0
+        name: Spellcheck
+        with:
+          source_files: README.md CHANGELOG.md nextflow_schema.json assets/schema_input.json
+          task_name: Markdown
+          output_file: spellcheck-output.txt
 
-    - uses: actions/upload-artifact@v4
-      if: '!cancelled()'
-      name: Archive spellcheck output
-      with:
-        name: Spellcheck artifact
-        path: spellcheck-output.txt
+      - uses: actions/upload-artifact@v4
+        if: "!cancelled()"
+        name: Archive spellcheck output
+        with:
+          name: Spellcheck artifact
+          path: spellcheck-output.txt

.gitlab-ci.yml

@@ -8,4 +8,4 @@ pages:
     paths:
       - public
   rules:
-    - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+    - if: "$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH"

.pre-commit-config.yaml

@@ -3,8 +3,10 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        exclude: ^(tests/|utils/|docs/)
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:
       - id: editorconfig-checker
         alias: ec
+        exclude: ^(tests/|utils/|docs/)

.spellcheck.yaml

@@ -1,23 +1,23 @@
 matrix:
-- name: Markdown
-  sources:
-  - '!venv/**/*.md|**/*.md'
-  default_encoding: utf-8
-  aspell:
-    lang: en
-    ignore-case: true
-  dictionary:
-    encoding: utf-8
-    wordlists:
-    - .wordlist.txt
-  pipeline:
-  - pyspelling.filters.markdown:
-      markdown_extensions:
-      - pymdownx.superfences
-      - pymdownx.striphtml
-  - pyspelling.filters.html:
-      comments: false
-      ignores:
-      - code
-      - pre
-      - small
+  - name: Markdown
+    sources:
+      - "!venv/**/*.md|**/*.md"
+    default_encoding: utf-8
+    aspell:
+      lang: en
+      ignore-case: true
+    dictionary:
+      encoding: utf-8
+      wordlists:
+        - .wordlist.txt
+    pipeline:
+      - pyspelling.filters.markdown:
+          markdown_extensions:
+            - pymdownx.superfences
+            - pymdownx.striphtml
+      - pyspelling.filters.html:
+          comments: false
+          ignores:
+            - code
+            - pre
+            - small

CHANGELOG.md

@@ -25,7 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - RASUSA now used for down sampling of Nanopore or PacBio data. [PR 125](https://github.com/phac-nml/mikrokondo/pull/125)
 
-- Default *Listeria* quality control parameters apply only to *monocytogenes* now. [PR 142](https://github.com/phac-nml/mikrokondo/pull/142)
+- Default _Listeria_ quality control parameters apply only to _monocytogenes_ now. [PR 142](https://github.com/phac-nml/mikrokondo/pull/142)
 
 ### `Updated`
 
@@ -57,7 +57,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Changed default option for `override_allele_scheme` from `null` to "" (evaluates to false). [PR 109](https://github.com/phac-nml/mikrokondo/pull/109)
 
-
 ## [0.4.0] - 2024-09-04
 
 ### `Changed`
@@ -72,7 +71,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Moved allele schema parameters under one option in the nextflow_schema.json. See [PR 104](https://github.com/phac-nml/mikrokondo/pull/104)
 
-
 ### `Fixed`
 
 - Fixed typo in metagenomic QC message. See [PR 103](https://github.com/phac-nml/mikrokondo/pull/103)
@@ -113,7 +111,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Altered name of stored `SpeciesTopHit` field in the irida-next.config, and added a field displaying the field name used addressing [PR 90](https://github.com/phac-nml/mikrokondo/pull/90)
 
-
 ## [0.2.1] - 2024-06-03
 
 ### `Fixed`

fontlist-v330.json

@@ -991,4 +991,5 @@
     }
   ],
   "__class__": "FontManager"
-}
+}
+

modules.json

@@ -1,27 +1,27 @@
 {
-    "name": "mk-kondo/mikrokondo",
-    "homePage": "https://github.com/mk-kondo/mikrokondo",
-    "repos": {
-        "https://github.com/nf-core/modules.git": {
-            "modules": {
-                "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
-                    },
-                    "fastqc": {
-                        "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
-                    },
-                    "multiqc": {
-                        "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
-                        "installed_by": ["modules"]
-                    }
-                }
-            }
+  "name": "mk-kondo/mikrokondo",
+  "homePage": "https://github.com/mk-kondo/mikrokondo",
+  "repos": {
+    "https://github.com/nf-core/modules.git": {
+      "modules": {
+        "nf-core": {
+          "custom/dumpsoftwareversions": {
+            "branch": "master",
+            "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+            "installed_by": ["modules"]
+          },
+          "fastqc": {
+            "branch": "master",
+            "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+            "installed_by": ["modules"]
+          },
+          "multiqc": {
+            "branch": "master",
+            "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+            "installed_by": ["modules"]
+          }
         }
+      }
     }
+  }
 }

modules/local/quast_assembly.nf

@@ -20,7 +20,7 @@ process QUAST {
     def args =  task.ext.args ?: ""
     def reads = null
     prefix = meta.id
-    
+
     def quast_table_name = "${params.quast.report_prefix}${meta.id}${params.quast.report_ext}"
 
     def long_read_string = "--single"
@@ -67,3 +67,4 @@ process QUAST {
     """
 
 }
+