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Add apbs (nf-core#10185)
* init apbs * updated in and out params and test files (locally) * meta yml updated and passing linting * sourcing files from test-datasets repo * review fixes
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‎modules/nf-core/apbs/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- conda-forge::apbs=3.4.1

‎modules/nf-core/apbs/main.nf‎

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process APBS {
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tag "$meta.id"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/28/288b945c2895993a166b5baf67efd85f2111a3efe64bd189dae731e697eae9ef/data':
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'community.wave.seqera.io/library/apbs:3.4.1--298b75172827aae7' }"
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input:
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tuple val(meta), path(apbs_input), path(pqr)
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output:
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tuple val(meta), path("*.dx") , emit: dx, optional: true
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tuple val(meta), path("io.mc") , emit: mc
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tuple val(meta), path("${prefix}.log"), emit: log
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tuple val("${task.process}"), val('apbs'), eval("apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\$||'"), topic: versions, emit: versions_apbs
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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apbs \\
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$args \\
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${apbs_input} \\
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2>&1 | tee ${prefix}.log
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"""
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stub:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo ${args}
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touch ${prefix}.dx
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touch ${prefix}.log
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"""
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}

‎modules/nf-core/apbs/meta.yml‎

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name: "apbs"
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description: |
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Compute biomolecular electrostatics by solving the Poisson-Boltzmann equation
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using APBS (Adaptive Poisson-Boltzmann Solver). Produces electrostatic potential
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maps and solvation energy values for large biomolecular assemblages.
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keywords:
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- electrostatics
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- poisson-boltzmann
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- solvation
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- structural-biology
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- biophysics
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- computational-chemistry
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tools:
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- "apbs":
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description: |
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APBS (Adaptive Poisson-Boltzmann Solver) is a software package for modelling
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biomolecular solvation through solution of the Poisson-Boltzmann equation.
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It computes electrostatic solvation energies and potentials for large
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biomolecular assemblages and is widely used in structural biology and
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computational biophysics.
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homepage: "https://www.poissonboltzmann.org/"
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documentation: "https://apbs.readthedocs.io/en/latest/"
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tool_dev_url: "https://github.com/Electrostatics/apbs"
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licence:
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- "Custom"
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identifier: ""
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- apbs_input:
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type: file
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description: |
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APBS input configuration file specifying the electrostatics calculation,
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including paths to molecular structure files (PQR/PDB) and calculation
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parameters. The file extension is typically `.in` but `.inp` is also
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accepted for legacy purposes.
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pattern: "*.{in,inp}"
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ontologies: []
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- pqr:
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type: file
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description: |
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One or more PQR molecular structure files referenced by the input
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configuration file. PQR files contain atomic coordinates, charges, and
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radii used by APBS for electrostatics calculations.
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pattern: "*.pqr"
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ontologies:
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- edam: "http://edamontology.org/format_4035" # PQR
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output:
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dx:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- "*.dx":
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type: file
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description: |
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OpenDX format volumetric electrostatic potential map file output by APBS.
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Optional: this output is only produced when the input configuration file
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contains a `write pot dx <dx_filename>` directive.
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pattern: "*.dx"
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ontologies: []
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mc:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- io.mc:
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type: file
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description: |
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APBS multigrid calculation output file containing energy and force
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information from the finite difference solver.
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pattern: "io.mc"
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ontologies: []
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log:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. `[ id:'sample1' ]`
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- ${prefix}.log:
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type: file
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description: |
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APBS standard output log file containing calculation results, including
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electrostatic solvation energies and run diagnostics.
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pattern: "*.log"
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ontologies:
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- edam: "http://edamontology.org/format_2330" # Textual format
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versions_apbs:
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- - ${task.process}:
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type: string
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description: The name of the process
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- apbs:
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type: string
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description: The name of the tool
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- apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\$||':
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type: eval
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description: The expression to obtain the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The name of the process
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- apbs:
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type: string
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description: The name of the tool
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- apbs --version 2>&1 | sed '6!d;s|^.*Version APBS ||; s| .*\$||':
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type: eval
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description: The expression to obtain the version of the tool
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authors:
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- "@vagkaratzas"
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maintainers:
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- "@vagkaratzas"

‎modules/nf-core/apbs/tests/main.nf.test‎

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nextflow_process {
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name "Test Process APBS"
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script "../main.nf"
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process "APBS"
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tag "modules"
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tag "modules_nfcore"
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tag "apbs"
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test("apbs - in_pqr - dx") {
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'proteomics/apbs/apbs-mol.in', checkIfExists: true),
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[
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file(params.modules_testdata_base_path + 'proteomics/apbs/methanol.pqr', checkIfExists: true),
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file(params.modules_testdata_base_path + 'proteomics/apbs/methoxide.pqr', checkIfExists: true)
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]
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]
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"""
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}
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}
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then {
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assert process.success
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assertAll(
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{ assert snapshot(
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process.out.dx,
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file(process.out.mc[0][1]).name,
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path(process.out.log[0][1]).readLines().size(),
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process.out.findAll { key, val -> key.startsWith("versions")}
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).match() }
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)
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}
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}
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test("apbs - in_pqr - dx - stub") {
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options "-stub"
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when {
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process {
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"""
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input[0] = [
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[ id:'test' ],
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file(params.modules_testdata_base_path + 'proteomics/apbs/apbs-mol.in', checkIfExists: true),
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[
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file(params.modules_testdata_base_path + 'proteomics/apbs/methanol.pqr', checkIfExists: true),
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file(params.modules_testdata_base_path + 'proteomics/apbs/methoxide.pqr', checkIfExists: true)
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]
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]
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"""
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}
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}
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then {
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assert process.success
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assertAll(
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{ assert snapshot(
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process.out.dx,
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process.out.log,
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file(process.out.mc[0][1]).name,
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process.out.findAll { key, val -> key.startsWith("versions")}
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).match() }
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)
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}
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}
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}

‎modules/nf-core/apbs/tests/main.nf.test.snap‎

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{
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"apbs - in_pqr - dx": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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[
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"pot1.dx:md5,2ec2b21c409dd3c5ae68be8202c23c97",
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"pot2.dx:md5,cdf35de3034b04e1710181c52be4a925",
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"pot3.dx:md5,810e4195370115e5f2539a6bc5297b40",
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"pot4.dx:md5,455718702c1b0b83a42cf4d6b8639fde"
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]
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]
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],
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"io.mc",
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221,
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{
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"versions_apbs": [
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[
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"APBS",
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"apbs",
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"3.4.1"
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]
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]
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2026-02-23T12:46:25.40825314"
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},
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"apbs - in_pqr - dx - stub": {
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"content": [
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[
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[
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{
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"id": "test"
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},
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"test.dx:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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[
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[
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{
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"id": "test"
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},
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"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"io.mc",
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{
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"versions_apbs": [
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[
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"APBS",
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"apbs",
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"3.4.1"
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]
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]
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.10.2"
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},
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"timestamp": "2026-02-23T12:46:56.301493133"
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}
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}

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