Merge pull request #179 from Daniel-VM/fix_linting_test_name

fixed matrix.test_name in linting and missing features from template 3.0.2
nf-core · Nov 5, 2024 · 02bf3dd · 02bf3dd
2 parents efe6309 + aa42f95
commit 02bf3dd
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Showing 10 changed files with 67 additions and 35 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,6 +35,10 @@ jobs:
           - "singularity"
         test_name:
           - "test"
+          - "test_long"
+          - "test_long_miniasm"
+          - "test_hybrid"
+          - "test_dfast"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -43,12 +47,6 @@ jobs:
             profile: "conda"
           - isMaster: false
             profile: "singularity"
-        parameters:
-          - "test"
-          - "test_long"
-          - "test_long_miniasm"
-          - "test_hybrid"
-          - "test_dfast"
 
     steps:
       - name: Check out pipeline code

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#179](https://github.com/nf-core/bacass/pull/179) Fixed matrix.test_name in linting and missing features from template 3.0.2.
 - [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample.
 - [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel.
 - [#168](https://github.com/nf-core/bacass/pull/168) Fix wrong metadata in canu input channel.

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -19,7 +19,6 @@
                 "anyOf": [
                     {
                         "type": ["string", "null"],
-                        "exists": true,
                         "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$"
                     },
                     {
@@ -33,7 +32,6 @@
                 "anyOf": [
                     {
                         "type": ["string", "null"],
-                        "exists": true,
                         "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$"
                     },
                     {
@@ -47,7 +45,6 @@
                 "anyOf": [
                     {
                         "type": ["string", "null"],
-                        "exists": true,
                         "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$"
                     },
                     {
@@ -61,7 +58,6 @@
                 "anyOf": [
                     {
                         "type": ["string", "null"],
-                        "exists": true,
                         "pattern": "^(\\/[\\S\\s]*|NA)$"
                     },
                     {

diff --git a/conf/test_dfast.config b/conf/test_dfast.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test_dfast profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv'
 

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -10,6 +10,15 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'

diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid.tsv'
 

diff --git a/conf/test_hybrid_dragonflye.config b/conf/test_hybrid_dragonflye.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test hybrid-dragonflye profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid_dragonflye.tsv'
 

diff --git a/conf/test_long.config b/conf/test_long.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test_long profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'
 

diff --git a/conf/test_long_dragonflye.config b/conf/test_long_dragonflye.config
@@ -9,6 +9,14 @@
 
 ----------------------------------------------------------------------------------------
 */
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
 
 params {
     config_profile_name        = 'Test_long_dragonfyle profile'

diff --git a/conf/test_long_miniasm.config b/conf/test_long_miniasm.config
@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test_long_miniasm profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv'