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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/differentialabundance Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
study_name = 'study'
study_type = 'rnaseq'
study_abundance_type = 'counts'
contrasts = null
querygse = null
matrix = null
transcript_length_matrix = null
control_features = null
sizefactors_from_controls = false
// Reporting
logo_file = "$projectDir/docs/images/nf-core-differentialabundance_logo_light.png"
css_file = "$projectDir/assets/nf-core_style.css"
citations_file = "$projectDir/CITATIONS.md"
report_file = "$projectDir/assets/differentialabundance_report.Rmd"
report_title = null
report_author = null
report_contributors = null
report_description = null
report_scree = true
report_round_digits = 4
// Sample sheet options
observations_type = 'sample'
observations_id_col = 'sample'
observations_name_col = null
// Feature options
features = null
features_type = 'gene'
features_id_col = 'gene_id'
features_name_col = 'gene_name'
features_metadata_cols = 'gene_id,gene_name,gene_biotype'
// GTF parsing options
features_gtf_feature_type = 'transcript'
features_gtf_table_first_field = 'gene_id'
// Affy-specific options
affy_cel_files_archive = null
affy_file_name_col = 'file'
affy_background = true
affy_bgversion = 2
affy_destructive = false
affy_cdfname = null
affy_rm_mask = false
affy_rm_outliers = false
affy_rm_extra = false
affy_build_annotation = true
// Proteus-specific options
proteus_measurecol_prefix = 'LFQ intensity'
proteus_norm_function = 'normalizeMedian'
proteus_plotsd_method = 'violin'
proteus_plotmv_loess = true
proteus_palette_name = 'Set1'
// Filtering options
filtering_min_samples = 1.0
filtering_min_abundance = 1.0
filtering_min_proportion = null
filtering_grouping_var = null
filtering_min_proportion_not_na = 0.5
filtering_min_samples_not_na = null
// Exploratory options
exploratory_main_variable = 'auto_pca'
exploratory_clustering_method = "ward.D2"
exploratory_cor_method = "spearman"
exploratory_n_features = 500
exploratory_whisker_distance = 1.5
exploratory_mad_threshold = -5
exploratory_assay_names = "raw,normalised,variance_stabilised"
exploratory_final_assay = "variance_stabilised"
exploratory_log2_assays = 'raw,normalised'
exploratory_palette_name = 'Set1'
// Differential options
differential_file_suffix = null
differential_feature_id_column = "gene_id"
differential_feature_name_column = "gene_name"
differential_fc_column = "log2FoldChange"
differential_pval_column = "pvalue"
differential_qval_column = "padj"
differential_min_fold_change = 2.0
differential_max_pval = 1.0
differential_max_qval = 0.05
differential_foldchanges_logged = true
differential_palette_name = 'Set1'
differential_subset_to_contrast_samples = false
// DESeq2-specific options
deseq2_test = "Wald"
deseq2_fit_type = "parametric"
deseq2_sf_type = 'ratio'
deseq2_min_replicates_for_replace = 7
deseq2_use_t = false
deseq2_lfc_threshold = 0
deseq2_alt_hypothesis = 'greaterAbs'
deseq2_independent_filtering = true
deseq2_p_adjust_method = 'BH'
deseq2_alpha = 0.1
deseq2_minmu = 0.5
deseq2_vs_method = 'vst' // 'rlog', 'vst', or 'rlog,vst'
deseq2_shrink_lfc = true
deseq2_cores = 1
deseq2_vs_blind = true
deseq2_vst_nsub = 1000
// Limma-specific options
limma_ndups = null
limma_spacing = null
limma_block = null
limma_correlation = null
limma_method = 'ls'
limma_proportion = 0.01
limma_stdev_coef_lim = '0.1,4'
limma_trend = false
limma_robust = false
limma_winsor_tail_p = '0.05,0.1'
limma_adjust_method = "BH"
limma_p_value = 1.0
limma_lfc = 0
limma_confint = false
// GSEA options
gsea_run = false
gsea_nperm = 1000
gsea_permute = 'phenotype'
gsea_scoring_scheme = 'weighted'
gsea_metric = 'Signal2Noise'
gsea_sort = 'real'
gsea_order = 'descending'
gsea_set_max = 500
gsea_set_min = 15
gsea_norm = 'meandiv'
gsea_rnd_type = 'no_balance'
gsea_make_sets = true
gsea_median = false
gsea_num = 100
gsea_plot_top_x = 20
gsea_rnd_seed = 'timestamp'
gsea_save_rnd_lists = false
gsea_zip_report = false
// gprofiler2 options
gprofiler2_run = false
gprofiler2_organism = null
gprofiler2_significant = true
gprofiler2_measure_underrepresentation = false
gprofiler2_correction_method = 'gSCS'
gprofiler2_sources = null
gprofiler2_evcodes = false
gprofiler2_max_qval = 0.05
gprofiler2_token = null
gprofiler2_background_file = 'auto'
gprofiler2_background_column = null
gprofiler2_domain_scope = 'annotated'
gprofiler2_min_diff = 1
gprofiler2_palette_name = 'Blues'
// ShinyNGS
shinyngs_build_app = true
shinyngs_guess_unlog_matrices = true
// Note: for shinyapps deployment, in addition to setting these values,
// SHINYAPPS_TOKEN and SHINYAPPS_SECRET must be available to the
// environment, probably via Nextflow secrets
shinyngs_deploy_to_shinyapps_io = false
shinyngs_shinyapps_account = null
shinyngs_shinyapps_app_name = null
// Gene set options
gene_sets_files = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
// 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
version = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/differentialabundance custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/differentialabundance.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/differentialabundance profiles: ${params.custom_config_base}/pipeline/differentialabundance.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
conda.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
conda.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
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
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_nogtf { includeConfig 'conf/test_nogtf.config' }
test_full { includeConfig 'conf/test_full.config' }
affy { includeConfig 'conf/affy.config' }
maxquant { includeConfig 'conf/maxquant.config' }
rnaseq { includeConfig 'conf/rnaseq.config' }
soft {includeConfig 'conf/soft.config'}
test_affy { includeConfig 'conf/test_affy.config' }
test_maxquant { includeConfig 'conf/test_maxquant.config' }
test_soft {includeConfig 'conf/test_soft.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / 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'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// 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"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// 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/differentialabundance'
author = 'Oskar Wacker, Jonathan Manning'
homePage = 'https://github.com/nf-core/differentialabundance'
description = 'Differential abundance analysis'
mainScript = 'main.nf'
nextflowVersion = '!>=23.10.0'
version = '1.5.0'
doi = '10.5281/zenodo.7568000'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}