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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/proteinfold Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
mode = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, helixfold3}
use_gpu = false
split_fasta = false
// Alphafold2 parameters
alphafold2_mode = "standard"
max_template_date = "2020-05-14"
full_dbs = false // true full_dbs, false reduced_dbs
alphafold2_model_preset = "monomer" // for AF2 {monomer (default), monomer_casp14, monomer_ptm, multimer}
alphafold2_db = null
// Alphafold2 links
bfd_link = null
small_bfd_link = null
alphafold2_params_link = null
mgnify_link = null
pdb70_link = null
pdb_mmcif_link = null
pdb_obsolete_link = null
uniref30_alphafold2_link = null
uniref90_link = null
pdb_seqres_link = null
uniprot_sprot_link = null
uniprot_trembl_link = null
// Alphafold2 paths
bfd_path = null
small_bfd_path = null
alphafold2_params_path = null
mgnify_path = null
pdb70_path = null
pdb_mmcif_path = null
uniref30_alphafold2_path = null
uniref90_path = null
pdb_seqres_path = null
uniprot_path = null
// Colabfold parameters
colabfold_server = "webserver"
colabfold_model_preset = "alphafold2_ptm" // {'auto', 'alphafold2', 'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'}
num_recycles_colabfold = 3
use_amber = true
colabfold_db = null
db_load_mode = 0
host_url = null
use_templates = true
create_colabfold_index = false
// Colabfold links
colabfold_db_link = null
uniref30_colabfold_link = null
// Colabfold paths
colabfold_db_path = null
uniref30_colabfold_path = null
// Esmfold parameters
esmfold_db = null
esmfold_model_preset = "monomer"
num_recycles_esmfold = 4
// Esmfold links
esmfold_3B_v1 = null
esm2_t36_3B_UR50D = null
esm2_t36_3B_UR50D_contact_regression = null
// Esmfold paths
esmfold_params_path = null
// RoseTTAFold_All_Atom parameters
rosettafold_all_atom_db = null
// RoseTTAFold_All_Atom links
uniref30_rosettafold_all_atom_link = null
pdb100_rosettafold_all_atom_link = null
bfd_rosettafold_all_atom_path = null
rfaa_paper_weights_link = null
// RoseTTAFold_All_Atom paths
uniref30_rosettafold_all_atom_path = null
pdb100_rosettafold_all_atom_path = null
bfd_rosettafold_all_atom_path = null
rfaa_paper_weights_path = null
// Helixfold3 parameters
helixfold3_db = null
// Helixfold3 links
helixfold3_uniclust30_link = null
helixfold3_ccd_preprocessed_link = null
helixfold3_rfam_link = null
helixfold3_init_models_link = null
helixfold3_bfd_link = null
helixfold3_small_bfd_link = null
helixfold3_uniprot_sprot_link = null
helixfold3_uniprot_trembl_link = null
helixfold3_pdb_seqres_link = null
helixfold3_uniref90_link = null
helixfold3_mgnify_link = null
helixfold3_pdb_mmcif_link = null
helixfold3_pdb_obsolete_link = null
// Helixfold3 paths
helixfold3_uniclust30_path = null
helixfold3_ccd_preprocessed_path = null
helixfold3_rfam_path = null
helixfold3_init_models_path = null
helixfold3_bfd_path = null
helixfold3_small_bfd_path = null
helixfold3_uniprot_path = null
helixfold3_pdb_seqres_path = null
helixfold3_uniref90_path = null
helixfold3_mgnify_path = null
helixfold3_pdb_mmcif_path = null
helixfold3_maxit_src_path = null
// Foldseek params
foldseek_search = null
foldseek_easysearch_arg = null
// Process skipping options
skip_multiqc = false
skip_visualisation = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
if (params.use_gpu) {
docker.runOptions = '--gpus all'
} else {
docker.runOptions = '-u $(id -u):$(id -g)'
}
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
arm {
if (params.use_gpu) {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all'
} else {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
if (params.use_gpu) { singularity.runOptions = '--nv' }
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
if (params.use_gpu) { apptainer.runOptions = '--nv' }
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_alphafold2_split { includeConfig 'conf/test_alphafold_split.config' }
test_alphafold2_download { includeConfig 'conf/test_alphafold_download.config' }
test_colabfold_local { includeConfig 'conf/test_colabfold_local.config' }
test_colabfold_webserver { includeConfig 'conf/test_colabfold_webserver.config' }
test_colabfold_download { includeConfig 'conf/test_colabfold_download.config' }
test_esmfold { includeConfig 'conf/test_esmfold.config' }
test_split_fasta { includeConfig 'conf/test_split_fasta.config' }
test_full { includeConfig 'conf/test_full.config' }
test_full_alphafold2_standard { includeConfig 'conf/test_full.config' }
test_full_alphafold2_split { includeConfig 'conf/test_full_alphafold_split.config' }
test_full_alphafold2_multimer { includeConfig 'conf/test_full_alphafold_multimer.config' }
test_full_colabfold_local { includeConfig 'conf/test_full_colabfold_local.config' }
test_full_colabfold_webserver { includeConfig 'conf/test_full_colabfold_webserver.config' }
test_full_colabfold_multimer { includeConfig 'conf/test_full_colabfold_webserver_multimer.config' }
test_full_esmfold { includeConfig 'conf/test_full_esmfold.config' }
test_full_esmfold_multimer { includeConfig 'conf/test_full_esmfold_multimer.config' }
test_rosettafold_all_atom { includeConfig 'conf/test_rosettafold_all_atom.config' }
test_helixfold3 { includeConfig 'conf/test_helixfold3.config' }
}
// Load nf-core custom profiles from different Institutions
try {
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/proteinfold custom profiles from different institutions.
try {
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/proteinfold.config" : "/dev/null"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/proteinfold profiles: ${params.custom_config_base}/pipeline/proteinfold.config")
}
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
charliecloud.registry = 'quay.io'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/proteinfold'
author = """Athanasios Baltzis, Jose Espinosa-Carrasco, Harshil Patel"""
homePage = 'https://github.com/nf-core/proteinfold'
description = """Protein 3D structure prediction pipeline"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.04.2'
version = '1.2.0dev'
doi = '10.5281/zenodo.7629996'
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
beforeText = """
-\033[2m----------------------------------------------------\033[0m-
\033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m
\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m
\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m
\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m
\033[0;32m`._,._,\'\033[0m
\033[0;35m ${manifest.name} ${manifest.version}\033[0m
-\033[2m----------------------------------------------------\033[0m-
"""
afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/${manifest.name}/blob/master/CITATIONS.md
"""
}
summary {
beforeText = validation.help.beforeText
afterText = validation.help.afterText
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load modules config for pipeline specific modes
if (params.mode.toLowerCase().split(",").contains("alphafold2")) {
includeConfig 'conf/modules_alphafold2.config'
}
if (params.mode.toLowerCase().split(",").contains("colabfold")) {
includeConfig 'conf/modules_colabfold.config'
}
if (params.mode.toLowerCase().split(",").contains("esmfold")) {
includeConfig 'conf/modules_esmfold.config'
}
if (params.mode.toLowerCase().split(",").contains("rosettafold_all_atom")) {
includeConfig 'conf/modules_rosettafold_all_atom.config'
}
if (params.mode.toLowerCase().split(",").contains("helixfold3")) {
includeConfig 'conf/modules_helixfold3.config'
}
// Load links to DBs and parameters
includeConfig 'conf/dbs.config'