Set time constraints for most processes and reduce mem req for WGD (fixes #54)

main.nf

@@ -731,7 +731,8 @@ phymlPublish
 process ev01 {
     publishDir "${params.output}/parsimony", mode: 'copy'
     memory '4 GB'
-
+    time '30min'
+    
     input:
     file species_tree from phymlTree
     file domain_annotation from all_ipsTSV_ev01
@@ -1040,7 +1041,8 @@ process wgd_mcl{
     tag "$species - $databaseSpecies"
     module 'mcl'
     memory '8 GB'
-
+    time '1h'
+    
     input:
 	set file(blast_results), val(species), val(databaseSpecies) from new_species_blasts_tagged
     
@@ -1091,6 +1093,8 @@ process wgd_ksd_paranome{
     module 'paml'
     module 'fasttree'
 
+    time '1h'
+    
     memory { 4.GB + 2.GB * task.attempt }
     errorStrategy 'retry'
     maxRetries 4
@@ -1121,9 +1125,11 @@ process wgd_ksd_one_v_one{
     module 'paml'
     module 'fasttree'
 
-    memory { 4.GB + 2.GB * task.attempt }
+    time '1h'
+    
+    memory { 1.GB + 1.GB * task.attempt }
     errorStrategy 'retry'
-    maxRetries 4
+    maxRetries 5
 
     cpus 4
 
@@ -1150,6 +1156,7 @@ process wgd_gmm{
     publishDir "${params.output}/wgd/${species}", mode: 'copy'
     tag "$species"
 
+    time '1h'
     memory '6 GB'
 
     input:
@@ -1170,6 +1177,7 @@ process wgd_bgmm{
     publishDir "${params.output}/wgd/${species}", mode: 'copy'
     tag "$species"
 
+    time '1h'
     memory '6 GB'
 
     input:
@@ -1188,6 +1196,7 @@ process wgd_kde{
     publishDir "${params.output}/wgd/${species}", mode: 'copy'
     tag "$species"
 
+    time '1h'
     memory '6 GB'
 
     input: