cloudprofile nextflow-version-error papanikos fix

configs/local.config

@@ -2,22 +2,22 @@ process {
     withLabel: altair           { cpus = 1 }
     withLabel: chromomap        { cpus = params.cores }
     withLabel: checkV           { cpus = params.cores }
-    withLabel: deepvirfinder    { cpus = 4 }
+    withLabel: deepvirfinder    { cpus = params.cores }
     withLabel: emboss           { cpus = params.cores }
     withLabel: ggplot2          { cpus = 1 }
     withLabel: hmmscan          { cpus = params.cores }
-    withLabel: marvel           { cpus = 4 }
-    withLabel: metaphinder      { cpus = 4 }
-    withLabel: pprmeta          { cpus = 4 }
-    withLabel: prodigal         { cpus = 1 }
+    withLabel: marvel           { cpus = params.cores }
+    withLabel: metaphinder      { cpus = params.cores }
+    withLabel: pprmeta          { cpus = params.cores }
+    withLabel: prodigal         { cpus = 4 }
     withLabel: python           { cpus = 1 }
     withLabel: r_plot           { cpus = 1 }
     withLabel: samtools         { cpus = 1 }
     withLabel: seqkit           { cpus = 1 }
-    withLabel: sourmash         { cpus = 4 }
+    withLabel: sourmash         { cpus = params.cores }
     withLabel: ubuntu           { cpus = 1 }
     withLabel: upsetr           { cpus = 1 }
-    withLabel: vibrant          { cpus = 4 }
+    withLabel: vibrant          { cpus = params.cores }
     withLabel: virfinder        { cpus = params.cores }
     withLabel: virnet           { cpus = params.cores }
     withLabel: virsorter        { cpus = params.cores }

configs/node.config

@@ -13,7 +13,7 @@ process {
     withLabel: prodigal         { cpus = 4; memory = '8 GB' }
     withLabel: python           { cpus = 2; memory = '3 GB' }
     withLabel: r_plot           { cpus = 4; memory = '4 GB' }
-    withLabel: samtools         { cpus = 1 ; memory = '32 GB' }
+    withLabel: samtools         { cpus = 4 ; memory = '6 GB' }
     withLabel: seqkit           { cpus = 1 ; memory = '4 GB' }
     withLabel: sourmash         { cpus = 8 ; memory = '32 GB' }
     withLabel: ubuntu           { cpus = 4; memory = '4 GB' }

modules/databases/download_pvog_DB.nf

@@ -1,6 +1,6 @@
 process pvog_DB {
     label 'noDocker'    
-    if (params.cloudProcess) { publishDir "${params.databases}/", mode: 'copy'}
+    if (params.cloudProcess) { publishDir "${params.databases}/pvogs/", mode: 'copy'}
     else { storeDir "${params.databases}/pvog" }  
     output:
         path("pvogs", type: 'dir')

modules/databases/download_references.nf

@@ -1,7 +1,7 @@
 process download_references {
+    label 'noDocker'
     if (params.cloudProcess) { publishDir "${params.databases}/references/", mode: 'copy', pattern: "phage_references.fa" }
-    else { storeDir "${params.databases}/references/" }
-    label 'noDocker'    
+    else { storeDir "${params.databases}/references/" }    
     output:
         path("phage_references.fa")
     script:

modules/parser/filter_virsorter2.nf

@@ -6,7 +6,7 @@ process filter_virsorter2 {
         tuple val(name), path("virsorter2_*.txt")
     shell:
         """
-        tail -n+2 *.tsv | awk '\$2>=${params.vs2_filter}' | awk '{ print \$1 }'  > virsorter2_\${PWD##*/}.txt
+        tail -n+2 *.tsv | awk '\$2>=${params.vs2_filter}' | awk '{ print \$1 }' | cut -d'|' -f1  > virsorter2_\${PWD##*/}.txt
         """
 }
 

nextflow.config

@@ -119,6 +119,28 @@ profiles {
         includeConfig 'configs/node.config'
     }
 
+    ukj_cloud { 
+        workDir = params.workdir
+        params.cloudProcess = true
+        docker { enabled = true } 
+        process.executor = 'google-lifesciences'
+        params.databases = 'gs://persistant-storage/What-the-Phage'
+        bucketDir = 'gs://case-tmp-dir/What-the-Phage'
+        google {  
+            project = 'case-dev-302214'
+            zone = 'europe-west1-b'
+            lifeSciences.preemptible = true
+            lifeSciences.bootDiskSize = 20.GB
+            }
+        includeConfig 'configs/container.config'
+        includeConfig 'configs/node.config'
+
+        // cloud error strategy
+        process.errorStrategy = { task.exitStatus in [10,14,143,137,104,134,139] ? 'retry' : 'terminate' }
+        process.maxRetries = 3
+        process { withLabel: noDocker           { container = 'nanozoo/template:3.8--d089809' }}
+        }
+
     //engines
     docker {
         docker { enabled = true }

phage.nf

@@ -71,6 +71,7 @@ if ( workflow.profile == 'standard' ) { exit 1, "NO VALID EXECUTION PROFILE SELE
 
 if (
     workflow.profile.contains('singularity') ||
+    workflow.profile.contains('ukj_cloud') ||
     workflow.profile.contains('docker')
     ) { "engine selected" }
 else { exit 1, "No engine selected:  -profile EXECUTER,ENGINE" }
@@ -82,6 +83,7 @@ if (
     workflow.profile.contains('ebi') ||
     workflow.profile.contains('slurm') ||
     workflow.profile.contains('lsf') ||
+    workflow.profile.contains('ukj_cloud') ||
     workflow.profile.contains('git_action')
     ) { "executer selected" }
 else { exit 1, "No executer selected:  -profile EXECUTER,ENGINE" }