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change process configurations #2

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db50d0e
change process configurations
Birkinshaw Nov 21, 2025
93439c6
Modify error strategy and max retries for processes
Birkinshaw Nov 21, 2025
0afb0ca
Increase memory allocation for CountUniqueSequences
Birkinshaw Nov 21, 2025
b639b6e
Increase CPU allocation for CountUniqueSequences
Birkinshaw Nov 22, 2025
46eccab
Update nextflow.config
Birkinshaw Nov 22, 2025
2225457
Increase CPU allocation for Multimer_Inference process
Birkinshaw Nov 22, 2025
02b64b2
Configure Alphafold2 process in nextflow.config
Birkinshaw Dec 5, 2025
ee8aae2
Change publishDir mode from 'copy' to 'move'
Birkinshaw Jan 20, 2026
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12 changes: 6 additions & 6 deletions modules/alphafold.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ process ALPHAFOLD_Feature{

tag "${fasta}"
errorStrategy 'ignore'
publishDir "${params.outdir}/", mode: 'copy', pattern: "${fasta}/*.pkl"
publishDir "${params.outdir}", mode: 'copy', pattern: "${fasta}/msas/*"
publishDir "${params.outdir}/", mode: 'move', pattern: "${fasta}/*.pkl"
publishDir "${params.outdir}", mode: 'move', pattern: "${fasta}/msas/*"

input:
tuple val(fasta),path(fasta_file),val(preset)
Expand Down Expand Up @@ -53,10 +53,10 @@ process ALPHAFOLD_Inference{
label 'Alphafold2'
tag "${fasta}"

publishDir "${params.outdir}/", mode: 'copy', pattern: "${fasta}/*.pdb"
publishDir "${params.outdir}/", mode: 'copy', pattern: "${fasta}/*.json"
publishDir "${params.outdir}/", mode: 'copy', pattern: "${fasta}/*.pkl"
publishDir "${params.outdir}", mode: 'copy', pattern: "${fasta}/plots/*.pdf"
publishDir "${params.outdir}/", mode: 'move', pattern: "${fasta}/*.pdb"
publishDir "${params.outdir}/", mode: 'move', pattern: "${fasta}/*.json"
publishDir "${params.outdir}/", mode: 'move', pattern: "${fasta}/*.pkl"
publishDir "${params.outdir}", mode: 'move', pattern: "${fasta}/plots/*.pdf"

output:
path("${fasta}/*.pdb")
Expand Down
46 changes: 43 additions & 3 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,53 @@ profiles {
milton{
conda.enabled = true
cleanup = false

process {
withLabel:Alphafold2 {
module = 'alphafold/2.3.2'
cpus = 10
memory = '100 GB'
}

}

process {
withName: 'CountUniqueSequences' {
cpus = 4
memory = { 4.GB + 4.GB * task.attempt }
queue = 'regular'
time = '10.m'
errorStrategy = {
if (task.exitStatus in 137..140) return 'retry'
else return 'ignore'
}
maxRetries = 3
}
}

process {
withName: 'Multimer_Feature' {
cpus = 8
memory = { 40.GB + 20.GB * task.attempt }
queue = 'regular'
time = '5.h'
errorStrategy = {
if (task.exitStatus in 137..140) return 'retry'
else return 'ignore'
}
maxRetries = 4
}
}

process {
withName: 'Multimer_Inference' {
cpus = 14
memory = { 80.GB + 20.GB * task.attempt }
queue = 'gpuq'
time = '5.h'
errorStrategy = {
if (task.exitStatus in 137..140) return 'retry'
else return 'ignore'
}
maxRetries = 4
}
}
}
debug {
Expand Down