Removed the test_github profile as test can now be used

.github/workflows/ci.yml

@@ -58,4 +58,4 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_github,singularity --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results

conf/modules.config

@@ -358,6 +358,9 @@ process {
     // Set up of the polishing pipeline
     if (params.polishing_on) {
         withName: LONGRANGER_MKREF {
+            if(System.getenv('GITHUB_ACTION') != null ) {
+                container = "ghcr.io/sanger-tol/longranger:2.2.2-c4"
+            }
             publishDir = [
                 path: { "${params.outdir}/${meta.id}.${params.hifiasm}/polishing" },
                 mode: params.publish_dir_mode,
@@ -368,6 +371,9 @@ process {
         withName: LONGRANGER_ALIGN {
             // Keep in sync with `longranger_lsf_sanger.config`
             ext.args = "--disable-ui --nopreflight"
+            if(System.getenv('GITHUB_ACTION') != null ) {
+                container = "ghcr.io/sanger-tol/longranger:2.2.2-c4"
+            }
             publishDir = [
                 path: { "${params.outdir}/${meta.id}.${params.hifiasm}/polishing" },
                 mode: params.publish_dir_mode,
@@ -674,33 +680,4 @@ profiles {
             }
         }
     }
-
-    test_github {
-        process {
-            // Set up of the scaffolding pipeline
-            withName: 'YAHS' {
-                // Skip the initial assembly error correction step
-                ext.args = '-r 1000,2000,5000'
-            }
-
-            withName: '.*HIFIASM.*' {
-                // Skip bloom filter
-                ext.args = '--primary -f0'
-            }
-
-            withName: '.*OATK' {
-                // Set kmer size and minimal coverage
-                ext.args = "-k1001 -c5 -Ttmp"
-            }
-
-            if (params.polishing_on) {
-                withName: LONGRANGER_MKREF {
-                    container = "ghcr.io/sanger-tol/longranger:2.2.2-c4"
-                }
-                withName: LONGRANGER_ALIGN {
-                    container = "ghcr.io/sanger-tol/longranger:2.2.2-c4"
-                }
-            }
-        }
-    }
 }

conf/test.config

@@ -14,15 +14,14 @@ 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'
+    // Match resource limits with the ubuntu2204-4c runner
+    max_cpus   = 4
+    max_memory = '15.GB'
     max_time   = '6.h'
 
     // Input data
     input = "${projectDir}/assets/test.yaml"
     bed_chunks_polishing = 2
     organelles_on = true
-    polishing_on = true
     hifiasm_hic_on = true
 }

docs/usage.md

@@ -88,7 +88,7 @@ The pipeline can be tested locally using a provided small test dataset:
 ```
 git clone [email protected]:sanger-tol/genomeassembly.git
 cd genomeassembly/
-nextflow run main.nf -profile test_github,singularity --outdir ${OUTDIR} {OTHER ARGUMENTS}
+nextflow run main.nf -profile test,singularity --outdir ${OUTDIR} {OTHER ARGUMENTS}
 ```
 
 These command line steps will download the pipeline and run the test.

nextflow.config

@@ -173,7 +173,6 @@ profiles {
         executor.memory        = 60.GB
     }
     test          { includeConfig 'conf/test.config'      }
-    test_github   { includeConfig 'conf/test_github.config'  }
     test_full     { includeConfig 'conf/test_full.config' }
 }