Updated nextflow modules and better configuration

conf/spot-extraction-modules.config

@@ -28,8 +28,15 @@ params {
 
 process {
 
-    withName: "(.*)?RS_FISH" {
+    withName: "(.*)?SPOT_EXTRACTION:SPARK.*" {
+        // set container for all spark tasks
+        container = 'ghcr.io/janeliascicomp/rs-fish-spark:4d1b901'
         errorStrategy = 'terminate'
+    }
+
+    withName: "(.*)?SPOT_EXTRACTION:RS_FISH" {
+        errorStrategy = 'terminate'
+        container = 'ghcr.io/janeliascicomp/rs-fish-spark:4d1b901'
         ext.args = [
             "--minIntensity=${params.rsfish_min_intensity}",
             "--maxIntensity=${params.rsfish_max_intensity}",
@@ -40,6 +47,10 @@ process {
         ].join(' ')
     }
 
+    withName: "(.*)?SPOT_EXTRACTION:POST_RS_FISH" {
+        container = 'ghcr.io/janeliascicomp/post-rs-fish:v1'
+    }
+
 }
 
 def arg_value(arg_flag, arg_value) {

conf/stitching-modules.config

@@ -26,31 +26,31 @@ params {
 
 process {
 
-    withName:"(.*)?STITCHING:.*" {
+    withName: "(.*)?STITCHING:.*" {
         // all processes that run as part of the stitching workflow
         // use this container
-        ext.container = 'ghcr.io/janeliascicomp/stitching-spark:1.11.0-rc2'
+        container = 'ghcr.io/janeliascicomp/stitching-spark:1.11.0-rc2'
         errorStrategy = 'terminate'
     }
 
-    withName: "(.*)?SPARK_STARTMANAGER" {
+    withName: "(.*)?STITCHING:(.*)SPARK_STARTMANAGER" {
         errorStrategy = 'terminate'
         ext.spark_local_dir = params.spark_local_dir ? params.spark_local_dir : ''
         ext.sleep_secs = 2
     }
 
-    withName: "(.*)?SPARK_STARTWORKER" {
+    withName: "(.*)?STITCHING:(.*):SPARK_STARTWORKER" {
         errorStrategy = 'terminate'
         ext.sleep_secs = 2
     }
 
-    withName: "(.*)?SPARK_WAITFORMANAGER" {
+    withName: "(.*)?STITCHING:(.*):SPARK_WAITFORMANAGER" {
         errorStrategy = 'terminate'
         ext.sleep_secs = 2
         ext.max_wait_secs = 7200
     }
 
-    withName: "(.*)?SPARK_WAITFORWORKER" {
+    withName: "(.*)?STITCHING:(.*):SPARK_WAITFORWORKER" {
         errorStrategy = 'terminate'
         ext.sleep_secs = 2
         ext.max_wait_secs = 7200

modules.json

@@ -66,7 +66,7 @@
                     },
                     "spark_start": {
                         "branch": "main",
-                        "git_sha": "ce27f00338affaed60cbb37b4dc060f145297c23",
+                        "git_sha": "e3b9a6883f427176c180f32e45b268539bd5496c",
                         "installed_by": ["subworkflows"]
                     },
                     "spark_stop": {
@@ -82,7 +82,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
                         "installed_by": ["modules"]
                     }
                 }

modules/janelia/rs_fish/main.nf

@@ -1,6 +1,6 @@
 process RS_FISH {
     tag "${meta.id}"
-    container { task && task.ext.container ?: 'ghcr.io/janeliascicomp/rs-fish-spark:8f8954f' }
+    container { task && task.ext.container ?: 'ghcr.io/janeliascicomp/rs-fish-spark:4d1b901' }
     cpus { spark.driver_cores }
     memory { spark.driver_memory }