fix linting and adjust test resource managment

.github/workflows/ci.yml

@@ -116,7 +116,7 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Run pipeline with profile ${{ matrix.tests }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --max_memory '6.GB' --max_cpus 2 --spectrum_batch_size 5000 --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --spectrum_batch_size 5000 --outdir ./results
 
   # Define a second workflow only against main with additional tests: test_timstof and test_full
   profile_main:
@@ -150,4 +150,4 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Run pipeline with profile ${{ matrix.tests }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --max_memory '6.GB' --max_cpus 2 --spectrum_batch_size 5000 --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --spectrum_batch_size 5000 --outdir ./results

conf/test.config

@@ -12,9 +12,9 @@
 
 process {
     resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
+        cpus: 2,
+        memory: '6.GB',
+        time: '2.h'
     ]
 }
 

conf/test_ionannotator.config

@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '2.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test ion annotator profile'
     config_profile_description = 'Minimal test dataset to check pipeline function with ion annotator'
 
-    // 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 + 'mhcquant/testdata/HepG2_sample_sheet.tsv'
     fasta = params.pipelines_testdata_base_path + 'mhcquant/testdata/UP000005640_9606.fasta'

conf/test_mokapot.config

@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '2.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test Mokapot profile'
     config_profile_description = 'Minimal test dataset to check pipeline function with Mokapot'
 
-    // 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 + 'mhcquant/testdata/HepG2_sample_sheet.tsv'
     fasta = params.pipelines_testdata_base_path + 'mhcquant/testdata/UP000005640_9606.fasta'

conf/test_percolator.config

@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '2.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test Percolator profile'
     config_profile_description = 'Minimal test dataset to check pipeline function with MS2PIP'
 
-    // 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 + 'mhcquant/testdata/HepG2_sample_sheet.tsv'
     fasta = params.pipelines_testdata_base_path + 'mhcquant/testdata/UP000005640_9606.fasta'

conf/test_timstof.config

@@ -10,15 +10,19 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.GB',
+        time: '2.h'
+    ]
+}
+
 params {
     config_profile_name        = 'Test timsTOF profile'
     config_profile_description = 'Minimal test dataset to check pipeline function with timsTOF data'
 
-    // 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 + 'mhcquant/testdata/sample_sheet_timstof.tsv'
     fasta = params.pipelines_testdata_base_path + 'mhcquant/testdata/UP000005640_9606.fasta'

modules.json

@@ -12,7 +12,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "openms/decoydatabase": {
@@ -61,7 +61,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -71,7 +71,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

nextflow.config

@@ -220,7 +220,6 @@ profiles {
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load nf-core/mhcquant custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/mhcquant.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile

nextflow_schema.json

@@ -561,22 +561,22 @@
             "$ref": "#/$defs/input_output_options"
         },
         {
-            "$ref": "#/definitions/database_options"
+            "$ref": "#/$defs/database_options"
         },
         {
-            "$ref": "#/definitions/preprocessing"
+            "$ref": "#/$defs/preprocessing"
         },
         {
-            "$ref": "#/definitions/search_settings"
+            "$ref": "#/$defs/search_settings"
         },
         {
-            "$ref": "#/definitions/rescoring_settings"
+            "$ref": "#/$defs/rescoring_settings"
         },
         {
-            "$ref": "#/definitions/quantification_options"
+            "$ref": "#/$defs/quantification_options"
         },
         {
-            "$ref": "#/definitions/post_processing"
+            "$ref": "#/$defs/post_processing"
         },
         {
             "$ref": "#/$defs/institutional_config_options"

workflows/mhcquant.nf

@@ -41,7 +41,7 @@ include { OPENMS_IDMERGER                            } from '../modules/nf-core/
 include { OPENMS_IDSCORESWITCHER                     } from '../modules/nf-core/openms/idscoreswitcher/main.nf'
 include { OPENMS_IDFILTER as OPENMS_IDFILTER_Q_VALUE } from '../modules/nf-core/openms/idfilter/main'
 include { MULTIQC                                    } from '../modules/nf-core/multiqc/main'
-include { paramsSummaryMap                           } from 'plugin/nf-validation'
+include { paramsSummaryMap                           } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc                       } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML                     } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText                     } from '../subworkflows/local/utils_nfcore_mhcquant_pipeline'