Merge branch 'CW-4398-base-config' into 'dev'

Initialise base.config

Closes CW-4398

See merge request epi2melabs/workflows/wf-basecalling!92

base.config

@@ -0,0 +1,123 @@
+params {
+    wf {
+        basecaller_container = "ontresearch/dorado"
+        container_sha = "shae36d1b49fe470a60e006afad90bedd2fc2774a89"
+        bonito_container = "ontresearch/bonito"
+        bonito_sha = "shaea43ca2333f91fa78a823f640ba158e4268f1f98"
+        common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158"
+    }
+}
+
+
+// used by default for "standard" (docker) and singularity profiles,
+// other profiles may override.
+process {
+    withLabel:wf_basecalling {
+        container = "${params.wf.basecaller_container}:${params.wf.container_sha}"
+    }
+    withLabel:wf_common {
+        container = "ontresearch/wf-common:${params.wf.common_sha}"
+    }
+
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    // by default GPU tasks will run in serial to avoid GPU management.
+    // cluster and cloud users can remove this with -profile discrete_gpus.
+    // we use profiles to handle this as maxForks cannot be set dynamically
+    // see https://github.com/nextflow-io/nextflow/discussions/3806 and CW-1857
+    withLabel:gpu {
+        maxForks = 1
+    }
+}
+
+profiles {
+    // the "standard" profile is used implicitely by nextflow
+    // if no other profile is given on the CLI
+    standard {
+        docker {
+            enabled = true
+            // this ensures container is run as host user and group, but
+            //    also adds host user to the within-container group
+            runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
+        }
+        process."withLabel:gpu".containerOptions = "--gpus all"
+    }
+
+    // using singularity instead of docker
+    singularity {
+        singularity {
+            enabled = true
+            autoMounts = true
+            //envWhitelist = "" // if your cluster sets a variable to indicate which GPU has been assigned you will want to allow it here
+        }
+        process."withLabel:gpu".containerOptions = "--nv"
+    }
+
+
+    // keep stub conda profile to prevent unknown profile warning so users get a better error
+    conda {
+        conda.enabled = true
+    }
+
+
+    // Using AWS batch.
+    // May need to set aws.region and aws.batch.cliPath
+    awsbatch {
+        process {
+            executor = 'awsbatch'
+            queue = "${params.aws_queue}"
+            memory = "16 GB" // likely not enough!
+            withLabel:wf_common {
+                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
+            }
+            shell = ['/bin/bash', '-euo', 'pipefail']
+
+            // lift limit on simultaneous gpu jobs for cloud
+            // and ensure that the host mounts relevant driver bobbins inside the container
+            withLabel:gpu {
+                maxForks = null
+                containerOptions = "-e NVIDIA_DRIVER_CAPABILITIES=compute,utility --gpus all"
+            }
+            withLabel:wf_basecalling {
+                container = "${params.aws_image_prefix}-dorado:${params.wf.container_sha}"
+            }
+            withLabel:wf_bonito {
+                container = "${params.aws_image_prefix}-bonito:${params.wf.bonito_sha}"
+            }
+        }
+    }
+
+    // local profile for simplified development testing
+    local {
+        process.executor = 'local'
+    }
+
+    // lift limit on simultaneous gpu jobs
+    discrete_gpus {
+        process."withLabel:gpu".maxForks = null
+    }
+}
+
+
+timeline {
+  enabled = true
+  file = "${params.out_dir}/execution/timeline.html"
+  overwrite = true
+}
+report {
+  enabled = true
+  file = "${params.out_dir}/execution/report.html"
+  overwrite = true
+}
+trace {
+  enabled = true
+  file = "${params.out_dir}/execution/trace.txt"
+  overwrite = true
+}
+
+env {
+    PYTHONNOUSERSITE = 1
+    JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr"
+}
+
+cleanup = true

nextflow.config

@@ -1,15 +1,8 @@
-//
-// Notes to End Users.
-//
-// The workflow should run without editing this configuration file,
-// however there may be instances in which you wish to edit this
-// file for compute performance or other reasons. Please see:
-//
-//   https://nextflow.io/docs/latest/config.html#configuration
-//
-// for further help editing this file.
+// import profiles and workflow SHA from core
+includeConfig "base.config"
 
 
+// define workflow params
 params {
     help = false
     version = false
@@ -65,11 +58,6 @@ params {
     igv = false
 
     wf {
-        basecaller_container = "ontresearch/dorado"
-        container_sha = "shae36d1b49fe470a60e006afad90bedd2fc2774a89"
-        bonito_container = "ontresearch/bonito"
-        bonito_sha = "shaea43ca2333f91fa78a823f640ba158e4268f1f98"
-        common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158"
         example_cmd = [
             "--basecaller_cfg '[email protected]'",
             "--dorado_ext 'pod5'",
@@ -95,118 +83,3 @@ epi2melabs {
     tags = "basecalling,utility"
     icon = "faTty"
 }
-
-
-// used by default for "standard" (docker) and singularity profiles,
-// other profiles may override.
-process {
-    withLabel:wf_basecalling {
-        container = "${params.wf.basecaller_container}:${params.wf.container_sha}"
-    }
-    withLabel:wf_common {
-        container = "ontresearch/wf-common:${params.wf.common_sha}"
-    }
-
-    shell = ['/bin/bash', '-euo', 'pipefail']
-
-    // by default GPU tasks will run in serial to avoid GPU management.
-    // cluster and cloud users can remove this with -profile discrete_gpus.
-    // we use profiles to handle this as maxForks cannot be set dynamically
-    // see https://github.com/nextflow-io/nextflow/discussions/3806 and CW-1857
-    withLabel:gpu {
-        maxForks = 1
-    }
-}
-
-
-profiles {
-    // the "standard" profile is used implicitely by nextflow
-    // if no other profile is given on the CLI
-    standard {
-        docker {
-            enabled = true
-            // this ensures container is run as host user and group, but
-            //    also adds host user to the within-container group
-            runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
-        }
-        process."withLabel:gpu".containerOptions = "--gpus all"
-    }
-
-    // using singularity instead of docker
-    singularity {
-        singularity {
-            enabled = true
-            autoMounts = true
-            //envWhitelist = "" // if your cluster sets a variable to indicate which GPU has been assigned you will want to allow it here
-        }
-        process."withLabel:gpu".containerOptions = "--nv"
-    }
-
-
-    // keep stub conda profile to prevent unknown profile warning so users get a better error
-    conda {
-        conda.enabled = true
-    }
-
-
-    // Using AWS batch.
-    // May need to set aws.region and aws.batch.cliPath
-    awsbatch {
-        process {
-            executor = 'awsbatch'
-            queue = "${params.aws_queue}"
-            memory = "16 GB" // likely not enough!
-            withLabel:wf_common {
-                container = "${params.aws_image_prefix}-wf-common:${params.wf.common_sha}"
-            }
-            shell = ['/bin/bash', '-euo', 'pipefail']
-
-            // lift limit on simultaneous gpu jobs for cloud
-            // and ensure that the host mounts relevant driver bobbins inside the container
-            withLabel:gpu {
-                maxForks = null
-                containerOptions = "-e NVIDIA_DRIVER_CAPABILITIES=compute,utility --gpus all"
-            }
-            withLabel:wf_basecalling {
-                container = "${params.aws_image_prefix}-dorado:${params.wf.container_sha}"
-            }
-            withLabel:wf_bonito {
-                container = "${params.aws_image_prefix}-bonito:${params.wf.bonito_sha}"
-            }
-        }
-    }
-
-    // local profile for simplified development testing
-    local {
-        process.executor = 'local'
-    }
-
-    // lift limit on simultaneous gpu jobs
-    discrete_gpus {
-        process."withLabel:gpu".maxForks = null
-    }
-}
-
-
-timeline {
-  enabled = true
-  file = "${params.out_dir}/execution/timeline.html"
-  overwrite = true
-}
-report {
-  enabled = true
-  file = "${params.out_dir}/execution/report.html"
-  overwrite = true
-}
-trace {
-  enabled = true
-  file = "${params.out_dir}/execution/trace.txt"
-  overwrite = true
-}
-
-env {
-    PYTHONNOUSERSITE = 1
-    JAVA_TOOL_OPTIONS = "-Xlog:disable -Xlog:all=warning:stderr"
-}
-
-cleanup = true