Merge branch 'pre-commit' into 'main'

Pre-commit

See merge request !2

.gitignore

-tmp/*
\ No newline at end of file
+tmp/*

.gitlab-ci.yml

@@ -14,8 +14,8 @@ s3_access_test:
   image: minio/mc
   stage: access_test
   rules:
-    - changes: # TODO change where necessary
-      - image/*
+    - changes:  # TODO change where necessary
+        - image/*
   before_script:
     - mc alias set genomes $S3_ENDPOINT $S3_ACCESS_KEY $S3_SECRET_KEY
   script:
@@ -36,10 +36,11 @@ build_nginx_with_jbrowse_config_file:
   image: gcr.io/kaniko-project/executor:debug-v0.21.0
   stage: build_container
   before_script:
+    # yamllint disable-line rule:line-length
     - echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
   script:
-    - /kaniko/executor --cache=true --context $CI_PROJECT_DIR/image 
-      --dockerfile $CI_PROJECT_DIR/image/Dockerfile 
+    - /kaniko/executor --cache=true --context $CI_PROJECT_DIR/image
+      --dockerfile $CI_PROJECT_DIR/image/Dockerfile
       --destination $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
 
 kustomize_build_apply:
@@ -53,7 +54,8 @@ kustomize_build_apply:
     - cat deployment/jbrowse2-dep.yaml
     - kubectl apply -k deployment
     - kubectl -n $NS rollout restart deployment/jbrowse2
-    - kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2
+    - kubectl -n $NS wait --for=condition=available
+      --timeout=60s deploy/jbrowse2
     - kubectl -n $NS rollout status deployment/jbrowse2
   dependencies:
     - cluster_access_test

.pre-commit-config.yaml

+---
+repos:
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-merge-conflict
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+  - repo: https://github.com/bridgecrewio/checkov.git
+    rev: 3.2.73
+    hooks:
+      - id: checkov
+        args: [-d .]
+  - repo: https://github.com/Agilicus/pre-commit-hook-k8svalidate.git
+    rev: v0.2.0
+    hooks:
+      - id: k8svalidate
+        files: .yml$
+  - repo: https://github.com/Yelp/detect-secrets
+    rev: v1.4.0
+    hooks:
+      - id: detect-secrets

.vscode/extensions.json

@@ -4,6 +4,6 @@
         "visualstudioexptteam.vscodeintellicode",
         "tomoki1207.pdf",
         "christian-kohler.path-intellisense",
-	"nextflow.nextflow"
+	    "nextflow.nextflow"
     ]
 }

TODO.md

@@ -2,4 +2,4 @@
 
 - use htslib for bgzip and tabix
 - npx @jbrowse/cli add-assembly https://s3.embl.de/annelids/pdumv021_genome.fa.gz --name pdumv021
-- use SAMtools for faidx
\ No newline at end of file
+- use SAMtools for faidx

deployment/jbrowse2-dep.yml

@@ -17,7 +17,7 @@ spec:
         app: jbrowse2
     spec:
       imagePullSecrets:
-        - name: gitlab-token-auth 
+        - name: gitlab-token-auth
       containers:
         - name: jbrowse2
           image: ${CI_REGISTRY_IMAGE}:jbrowse2-${CI_COMMIT_SHORT_SHA}
@@ -28,7 +28,7 @@ spec:
               cpu: 1
             limits:
               memory: 4096Mi
-              cpu: 2
+              cpu: 1
           ports:
             - name: http
               containerPort: 80
@@ -70,4 +70,4 @@ spec:
                   name: http
   tls:
     - hosts:
-      - ${JBROWSE_HOSTNAME}
\ No newline at end of file
+        - ${JBROWSE_HOSTNAME}

deployment/kustomization.yaml

+---
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
 resources:
-- jbrowse2-dep.yaml
+  - jbrowse2-dep.yaml
 labels:
-- includeSelectors: true
-  pairs:
-    app: jbrowse2
+  - includeSelectors: true
+    pairs:
+      app: jbrowse2

resources/genomes.csv

 name,url
-pdumv021,https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz
\ No newline at end of file
+pdumv021,https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz

resources/variations.csv

 "/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN035.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf" 
+"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf"
 "/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN055.vcf"
 "/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN056.vcf"
 "/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN057.vcf"
@@ -17,4 +17,4 @@
 "/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN028.vcf"
 "/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN029.vcf"
 "/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN030.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN031.vcf"
\ No newline at end of file
+"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN031.vcf"