Fix Nextflow config syntax

CovertLab · Dec 3, 2024 · c9b1d12 · c9b1d12
1 parent 4717d95
commit c9b1d12
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Showing 2 changed files with 56 additions and 56 deletions.
diff --git a/runscripts/nextflow/config.template b/runscripts/nextflow/config.template
@@ -14,25 +14,36 @@ trace {
 
 profiles {
     gcloud {
-        // Retry once with more RAM if OOM
-        process.memory = { 4.GB * task.attempt }
-        // Using single core is slightly slower but much cheaper
-        process.cpus = 1
-        process.executor = 'google-batch'
-        process.container = params.container_image
-        // Necessary otherwise symlinks to other files in bucket can break
-        process.containerOptions = '--volume /mnt/disks/BUCKET:/mnt/disks/BUCKET'
         process {
             withLabel: parca {
                 cpus = params.parca_cpus
                 memory = params.parca_cpus * 2.GB
             }
+            errorStrategy = {
+                // Codes: 137 (out-of-memory), 50001 - 50006 (Google Batch task fail:
+                // https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes)
+                (((task.exitStatus == 137) || (task.exitStatus >= 50001 && task.exitStatus <= 50006))
+                && (task.attempt <= process.maxRetries)) ? 'retry' : 'ignore'
+            }
+            // Retry once with more RAM if OOM
+            memory = { 4.GB * task.attempt }
+            maxRetries = 1
+            // Using single core is slightly slower but much cheaper
+            cpus = 1
+            executor = 'google-batch'
+            container = params.container_image
+            // Necessary otherwise symlinks to other files in bucket can break
+            containerOptions = '--volume /mnt/disks/BUCKET:/mnt/disks/BUCKET'
+            // Check Google Cloud latest spot pricing / performance
+            machineType = {
+                def cpus = task.cpus
+                def powerOf2 = 1
+                while (powerOf2 < cpus && powerOf2 < 64) {
+                    powerOf2 *= 2
+                }
+                return "t2d-standard-${powerOf2}"
+            }
         }
-        process.errorStrategy = {
-            // Codes: 137 (out-of-memory), 50001 - 50006 (Google Batch task fail:
-            // https://cloud.google.com/batch/docs/troubleshooting#reserved-exit-codes)
-            (((task.exitStatus == 137) || (task.exitStatus >= 50001 && task.exitStatus <= 50006))
-            && (task.attempt <= process.maxRetries)) ? 'retry' : 'ignore' }
         // For this script to work on a Compute Engine VM, you must
         // - Set default Compute Engine region and zone for your project
         // - Set access scope to "Allow full access to all Cloud APIs" when
@@ -54,60 +65,51 @@ profiles {
         google.batch.subnetwork = "regions/${google.location}/subnetworks/default"
         docker.enabled = true
         params.projectRoot = '/vEcoli'
-        process.maxRetries = 1
-        // Check Google Cloud latest spot pricing / performance
-        process.machineType = { 
-            def cpus = task.cpus
-            def powerOf2 = 1
-            while (powerOf2 < cpus && powerOf2 < 64) {
-                powerOf2 *= 2
-            }
-            return "t2d-standard-${powerOf2}"
-        }
         workflow.failOnIgnore = true
     }
     sherlock {
-        process.memory = {
-            if ( task.exitStatus in [137, 140] ) {
-                4.GB * task.attempt
-            } else {
-                4.GB
-            }
-        }
-        process.errorStrategy = {
-            // Codes: 140 (SLURM job limits), 143 (SLURM preemption)
-            // Default value for exitStatus is max integer value, this
-            // is a catch-all for errors that leave no exit code
-            ((task.exitStatus in [140, 143, Integer.MAX_VALUE])
-            && (task.attempt <= process.maxRetries)) ? 'retry' : 'ignore' }
-        // Using single core is slightly slower but can have shorter
-        // queue times and is less damaging to future job priority
-        process.cpus = 1
-        process.executor = 'slurm'
-        process.queue = 'mcovert,owners'
-        process.container = params.container_image
-        apptainer.enabled = true
         process {
             // Run analyses, create variants, and run ParCa locally with
             // the job used to launch workflow to avoid long queue times
             withLabel: short {
                 executor = 'local'
-            },
+            }
             // ParCa 4 CPUs in ~15 min, 1 CPU in ~30 min, not too bad
             withLabel: parca {
                 executor = 'local'
                 cpus = 1
                 memory = 2.GB
             }
-        }
-        process.time = {
-            if ( task.exitStatus == 140 ) {
-                1.h * task.attempt
-            } else {
-                1.h
+            container = params.container_image
+            queue = 'mcovert,owners'
+            executor = 'slurm'
+            // Single core sims are slightly slower but can have shorter
+            // queue times and is less damaging to future job priority
+            cpus = 1
+            memory = {
+                if ( task.exitStatus in [137, 140] ) {
+                    4.GB * task.attempt
+                } else {
+                    4.GB
+                }
             }
+            time = {
+                if ( task.exitStatus == 140 ) {
+                    1.h * task.attempt
+                } else {
+                    1.h
+                }
+            }
+            errorStrategy = {
+                // Codes: 140 (SLURM job limits), 143 (SLURM preemption)
+                // Default value for exitStatus is max integer value, this
+                // is a catch-all for errors that leave no exit code
+                ((task.exitStatus in [140, 143, Integer.MAX_VALUE])
+                && (task.attempt <= process.maxRetries)) ? 'retry' : 'ignore'
+            }
+            maxRetries = 3
         }
-        process.maxRetries = 3
+        apptainer.enabled = true
         params.projectRoot = "${launchDir}"
         // Avoid getting queue status too frequently (can cause job status mixups)
         executor.queueStatInterval = '2 min'
@@ -127,15 +129,15 @@ profiles {
         workflow.failOnIgnore = true
     }
     standard {
-        process.executor = 'local'
         params.projectRoot = "${launchDir}"
         workflow.failOnIgnore = true
-        process.errorStrategy = 'ignore'
         process {
             withLabel: parca {
                 cpus = params.parca_cpus
                 memory = params.parca_cpus * 2.GB
             }
+            executor = 'local'
+            errorStrategy = 'ignore'
         }
     }
 }
diff --git a/runscripts/workflow.py b/runscripts/workflow.py
@@ -379,9 +379,7 @@ def main():
     nf_config = nf_config.replace(
         "PUBLISH_DIR", os.path.dirname(os.path.dirname(out_uri))
     )
-    nf_config = nf_config.replace(
-        "PARCA_CPUS", str(config["parca_options"]["cpus"])
-    )
+    nf_config = nf_config.replace("PARCA_CPUS", str(config["parca_options"]["cpus"]))
 
     # By default, assume running on local device
     nf_profile = "standard"