omic/bioemu
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Simplify workflow: separate processes per protein, avoid filter/map chains

Browse Source 
Split GENERATE_STRUCTURE into two explicit processes to avoid
channel filter/map/first() chains that cause StackOverflowError
in Nextflow 24.10.x
This commit is contained in:
Olamide Isreal
2026-03-26 14:55:33 +01:00
parent ce1f5dff03
commit e172ccc453
1 changed files with 47 additions and 22 deletions
Download Patch File Download Diff File Expand all files Collapse all files

69
main.nf
View File

@@ -1,7 +1,6 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl=2
// Define parameters — PVC mount paths for k8s execution
params.protein1_fasta = '/omic/eureka/bioemu/input/trp_cage.fasta'
params.protein2_fasta = '/omic/eureka/bioemu/input/villin_headpiece.fasta'
params.complex_name = 'protein_complex'
@@ -13,15 +12,16 @@ params.batch_size = 5
params.temperature = 300
params.n_clusters = 5
process GENERATE_STRUCTURE {
process GENERATE_STRUCTURE_1 {
container 'harbor.cluster.omic.ai/omic/bioemu:latest'
publishDir "${params.outdir}/${params.complex_name}", mode: 'copy'
publishDir "${params.outdir}/${params.complex_name}/protein1", mode: 'copy'
input:
tuple val(protein_id), path(fasta)
path fasta
output:
tuple val(protein_id), path("${protein_id}_topology.pdb"), path("${protein_id}_samples.xtc")
path "protein1_topology.pdb", emit: topology
path "protein1_samples.xtc", emit: samples
script:
"""
@@ -35,8 +35,36 @@ process GENERATE_STRUCTURE {
--output_dir . \\
--cache_embeds_dir ${params.cache_dir}
mv topology.pdb ${protein_id}_topology.pdb
mv samples.xtc ${protein_id}_samples.xtc
mv topology.pdb protein1_topology.pdb
mv samples.xtc protein1_samples.xtc
"""
}
process GENERATE_STRUCTURE_2 {
container 'harbor.cluster.omic.ai/omic/bioemu:latest'
publishDir "${params.outdir}/${params.complex_name}/protein2", mode: 'copy'
input:
path fasta
output:
path "protein2_topology.pdb", emit: topology
path "protein2_samples.xtc", emit: samples
script:
"""
SEQUENCE=\$(grep -v ">" ${fasta} | tr -d '\\n')
mkdir -p ${params.cache_dir}
python3 -m bioemu.sample \\
--sequence "\${SEQUENCE}" \\
--num_samples ${params.num_samples} \\
--batch_size_100 ${params.batch_size} \\
--output_dir . \\
--cache_embeds_dir ${params.cache_dir}
mv topology.pdb protein2_topology.pdb
mv samples.xtc protein2_samples.xtc
"""
}
@@ -68,26 +96,23 @@ process CALCULATE_BINDING {
--plot energy_comparison.png
echo "# Binding Free Energy Analysis: ${params.complex_name}" > binding_energy_report.txt
echo "======================================================" >> binding_energy_report.txt
echo "## Experimental Value: ${params.exp_dG} kcal/mol" >> binding_energy_report.txt
echo "" >> binding_energy_report.txt
echo "Experimental: ${params.exp_dG} kcal/mol" >> binding_energy_report.txt
PREDICTED_DG=\$(grep -A1 "binding_free_energy" binding_energy.csv | tail -n1 | cut -d',' -f2)
echo "## BioEmu Prediction: \${PREDICTED_DG} kcal/mol" >> binding_energy_report.txt
echo "Predicted: \${PREDICTED_DG} kcal/mol" >> binding_energy_report.txt
"""
}
workflow {
protein1_ch = Channel.fromPath(params.protein1_fasta)
.map { fasta -> tuple("protein1", fasta) }
protein2_ch = Channel.fromPath(params.protein2_fasta)
.map { fasta -> tuple("protein2", fasta) }
fasta1 = Channel.fromPath(params.protein1_fasta)
fasta2 = Channel.fromPath(params.protein2_fasta)
all_proteins = protein1_ch.mix(protein2_ch)
GENERATE_STRUCTURE_1(fasta1)
GENERATE_STRUCTURE_2(fasta2)
GENERATE_STRUCTURE(all_proteins)
p1 = GENERATE_STRUCTURE.out.filter { it[0] == "protein1" }.map { [it[1], it[2]] }.first()
p2 = GENERATE_STRUCTURE.out.filter { it[0] == "protein2" }.map { [it[1], it[2]] }.first()
CALCULATE_BINDING(p1[0], p1[1], p2[0], p2[1])
CALCULATE_BINDING(
GENERATE_STRUCTURE_1.out.topology,
GENERATE_STRUCTURE_1.out.samples,
GENERATE_STRUCTURE_2.out.topology,
GENERATE_STRUCTURE_2.out.samples
)
}