Commit e6c2b009 authored by Thomas Van Parys's avatar Thomas Van Parys
Browse files

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

parent 11546a31
......@@ -731,6 +731,7 @@ phymlPublish
process ev01 {
publishDir "${params.output}/parsimony", mode: 'copy'
memory '4 GB'
time '30min'
input:
file species_tree from phymlTree
......@@ -1040,6 +1041,7 @@ process wgd_mcl{
tag "$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:
......
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