add missing processes

PGScatalog · Oct 14, 2024 · 8b20b61 · 8b20b61
1 parent 38cad8b
commit 8b20b61
Showing 1 changed file with 125 additions and 113 deletions.
diff --git a/docs/how-to/bigjob.rst b/docs/how-to/bigjob.rst
@@ -79,119 +79,131 @@ on UK Biobank with a SLURM cluster:
 
 .. code-block:: text
 
-    process {
-      errorStrategy = 'retry'
-      maxRetries = 3
-      maxErrors = '-1'
-      executor = 'slurm'
-
-      withName: 'SAMPLESHEET_JSON' {
-        cpus = 1
-        memory = { 1.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'DOWNLOAD_SCOREFILES' {
-        cpus = 1
-        memory = { 1.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'COMBINE_SCOREFILES' {
-        cpus = 1
-        memory = { 16.GB * task.attempt }
-        time = { 2.hour * task.attempt }
-      }
-
-      withName: 'PLINK2_MAKEBED' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'RELABEL_IDS' {
-        cpus = 1
-        memory = { 16.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'PLINK2_ORIENT' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'DUMPSOFTWAREVERSIONS' {
-        cpus = 1
-        memory = { 1.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'ANCESTRY_ANALYSIS' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'SCORE_REPORT' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'EXTRACT_DATABASE' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'PLINK2_RELABELPVAR' {
-        cpus = 1
-        memory = { 16.GB * task.attempt }
-        time = { 2.hour * task.attempt }
-      }
-
-      withName: 'INTERSECT_VARIANTS' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'INTERSECT_THINNED' {
-        cpus = 1
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'MATCH_VARIANTS' {
-        cpus = 2
-        memory = { 32.GB * task.attempt }
-        time = { 6.hour * task.attempt }
-      }
-
-      withName: 'FILTER_VARIANTS' {
-        cpus = 1
-        memory = { 16.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'MATCH_COMBINE' {
-        cpus = 2
-        memory = { 64.GB * task.attempt }
-        time = { 6.hour * task.attempt }
-      }
-
-      withName: 'FRAPOSA_PCA' {
-        cpus = 2
-        memory = { 8.GB * task.attempt }
-        time = { 1.hour * task.attempt }
-      }
-
-      withName: 'PLINK2_SCORE' {
-        cpus = 2
-        memory = { 8.GB * task.attempt }
-        time = { 16.hour * task.attempt }
-      }
+  process {
+    errorStrategy = 'retry'
+    maxRetries = 3
+    maxErrors = '-1'
+    executor = 'slurm'
+
+    withName: 'SAMPLESHEET_JSON' {
+      cpus = 1
+      memory = { 1.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'DOWNLOAD_SCOREFILES' {
+      cpus = 1
+      memory = { 1.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'COMBINE_SCOREFILES' {
+      cpus = 1
+      memory = { 16.GB * task.attempt }
+      time = { 2.hour * task.attempt }
+    }
+
+    withName: 'PLINK2_MAKEBED' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'RELABEL_IDS' {
+      cpus = 1
+      memory = { 16.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'PLINK2_ORIENT' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'DUMPSOFTWAREVERSIONS' {
+      cpus = 1
+      memory = { 1.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'ANCESTRY_ANALYSIS' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'SCORE_REPORT' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'EXTRACT_DATABASE' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'PLINK2_RELABELPVAR' {
+      cpus = 1
+      memory = { 16.GB * task.attempt }
+      time = { 2.hour * task.attempt }
+    }
+
+    withName: 'INTERSECT_VARIANTS' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'INTERSECT_THINNED' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'MATCH_VARIANTS' {
+      cpus = 2
+      memory = { 32.GB * task.attempt }
+      time = { 6.hour * task.attempt }
+    }
+
+    withName: 'FILTER_VARIANTS' {
+      cpus = 1
+      memory = { 16.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'MATCH_COMBINE' {
+      cpus = 2
+      memory = { 64.GB * task.attempt }
+      time = { 6.hour * task.attempt }
+    }
+
+    withName: 'FRAPOSA_PCA' {
+      cpus = 2
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'PLINK2_SCORE' {
+      cpus = 2
+      memory = { 8.GB * task.attempt }
+      time = { 16.hour * task.attempt }
+    }
+
+    withName: 'FRAPOSA_PROJECT' {
+      cpus = 1
+      memory = { 8.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }
+
+    withName: 'SCORE_AGGREGATE' {
+      cpus = 1
+      memory = { 16.GB * task.attempt }
+      time = { 1.hour * task.attempt }
+    }    
   }