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