Refactor configs

.github/workflows/main.yml

@@ -21,7 +21,12 @@ jobs:
         sudo mv nextflow /usr/local/bin/
     - name: Run movp test
       run: |
-        nextflow run marine-omics/movp -profile docker,test -r main
+        nextflow run marine-omics/movp -profile docker,test -r main --callers gatk
+    - name: Whereami
+      if: always()
+      run: |
+      pwd
+      ls -a 
     - name: Archive nextflow log
       if: always()
       uses: actions/upload-artifact@v4

conf/setonix.config

@@ -0,0 +1,57 @@
+process {
+  cache = 'lenient'
+  stageInMode = 'symlink'
+
+  withName: 'fastq2ubam'{
+    cpus   = 1
+  }
+
+  withName: 'freebayes'{
+    cpus = 1
+    memory          =  20.GB 
+    ext.args='-m 20 -q 20 -R 0 -S 0'
+  }
+
+  withName: 'mpileup_call'{
+    cpus = 1
+    memory          = 10.GB 
+  }
+
+  withName: 'mpileup_collect'{
+    memory          = 40.GB 
+  }  
+
+  withName: 'freebayes_collect'{
+    memory          = 40.GB 
+  }
+
+
+}
+
+params {    
+    workDir = "$MYSCRATCH/nxf_work"
+
+
+
+    singularity {
+      enabled = true
+      envWhitelist = 'SINGULARITY_BINDPATH, SINGULARITYENV_LD_LIBRARY_PATH, SINGULARITYENV_LD_PRELOAD'
+      cacheDir = "$MYSOFTWARE/.nextflow_singularity"
+      runOptions = "--rocm"
+    }
+
+    slurm_account = 'pawsey1088'
+    process {
+      executor = 'slurm'
+      clusterOptions = "--account=${params.slurm_account}"
+      queue = 'work'
+      cpus = 1
+      time = '1h'
+      memory = '1800MB'
+
+    }
+executor {
+      $slurm {
+        queueSize = 1024
+      }
+    }

nextflow.config

@@ -58,6 +58,7 @@ profiles {
 
     zodiac { includeConfig 'conf/zodiac.config' }
     genomics { includeConfig 'conf/genomics.config' }
+    setonix { includeConfig 'conf/setonix.config' }    
 
 
 }