publishdir removed for some modules

Author: saulpierotti

conf/modules.config

@@ -528,6 +528,9 @@ process {
 
     withName: SAMTOOLS_INDEX {
         conda = null // temporary for mOTUs 4
+        publishDir = [
+            enabled: false
+        ]
     }
 
     withName: MERGE_RUNS {
@@ -553,7 +556,8 @@ process {
         tag        = { "${meta.db_name}|${meta.id}" }
         ext.prefix = { params.perform_runmerging ? "${meta.id}_${meta.db_name}" : "${meta.id}_${meta.run_accession}_${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/motus/${meta.db_name}/" },
+            path: { "${params.outdir}/motus/profile/${meta.db_name}/" },
+            pattern: '*.{out,log,mgc}',
             mode: params.publish_dir_mode,
         ]
     }
@@ -562,24 +566,35 @@ process {
         conda = null // temporary for mOTUs 4
         ext.prefix = { "${meta.id}_read${meta.paired_idx}_renamed_reads.${meta.is_fasta ? "fasta" : "fastq" }" }
         ext.args = "-c fastx '{sub(/\\/1\$|\\/2\$/, \"\", \$name); print \"@\"\$name\"\\n\"\$seq\"\\n+\\n\"\$qual}'"
+        publishDir = [
+            enabled: false
+        ]
     }
 
 
     withName: MOTUS_MERGE {
         ext.prefix = { "motus_${meta.id}_combined_reports" }
         memory = { 10.GB * task.attempt }
         publishDir = [
-            path: { "${params.outdir}/motus/" },
+            path: { "${params.outdir}/motus/merge/${meta.db_name}/" },
+            pattern: '*.txt',
             mode: params.publish_dir_mode,
         ]
     }
 
     withName: CAYMAN_PROFILE {
         conda = null // temporary for mOTUs 4
+        errorStrategy = {
+            // cayman returns error 1 for out of memory
+            sleep(Math.pow(2, task.attempt) * 200 as long)
+            return 'retry'
+        }
+        maxRetries = 10
         tag        = { "${meta.db_name}|${meta.id}" }
         ext.prefix = { params.perform_runmerging ? "${meta.id}_${meta.db_name}" : "${meta.id}_${meta.run_accession}_${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/cayman/${meta.db_name}/" },
+            path: { "${params.outdir}/cayman/profile/${meta.db_name}/" },
+            pattern: '*.{txt.gz,log}',
             mode: params.publish_dir_mode,
         ]
     }

conf/zellerlab.config

@@ -19,7 +19,7 @@ profiles {
         process {
             executor = 'slurm'
             errorStrategy = {
-                if (task.exitStatus in [132, 135] ) {
+                if (task.exitStatus in [132, 135, 255] ) {
                     sleep(Math.pow(2, task.attempt) * 200 as long)
                     return 'retry'
                 }