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nextflow.config
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/*
========================================================================================
kaitlinchaung/nomad Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
input = null
dataset = "dataset"
element_annotations_samplesheet = null
genome_index = null
transcriptome_index = null
gene_bed = null
star_index = null
gtf = null
is_RNA_seq = false
num_reads_first_pass = 4000000
num_reads_second_pass = 4000000
consensus_length = 200
kmer_size = 27
anchor_mode = "tile"
window_slide = 5
use_read_length = true
lookahead = null
direction = "down"
fdr_threshold = .05
run_type = "bulk"
stratify_level = 3
anchor_count_threshold = 50
K_num_hashes = 10
L_num_random_Cj = 50
anchor_unique_targets_threshold = 1
anchor_samples_threshold = 1
anchor_sample_counts_threshold = 5
num_decoy_anchors = 1000
all_anchors_pvals_file = true
anchors_file = null
is_10X = false
is_RNAseq = false
run_trimming = false
run_umitools = true
run_decoy = false
run_blast = false
run_annotations = false
run_anchor_target_counts = false
run_pvals_only = false
run_anchor_heatmaps = false
num_heatmap_anchors = 100
results_dir = null
use_heatmap_anchor_list = false
heatmap_anchor_list = null
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = false
fasta = "genome.fa"
// Trimming
clip_r1 = null
clip_r2 = null
three_prime_clip_r1 = null
three_prime_clip_r2 = null
trim_nextseq = null
save_trimmed = false
// MultiQC options
multiqc_config = null
multiqc_title = null
max_multiqc_email_size = '25.MB'
// Boilerplate options
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
help = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_description = null
config_profile_contact = null
config_profile_url = null
config_profile_name = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '828.GB'
max_cpus = 1
max_time = '240.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.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 igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
horence {
process.executor = 'slurm'
process.clusterOptions = '-p horence,quake,owners --requeue'
process.queueSize = 500
process.pollInterval = '3 min'
process.dumpInterval = '6 min'
process.queueStatInterval = '5 min'
process.exitReadTimeout = '13 min'
process.submitRateLimit = '5sec'
process.errorStrategy = { task.exitStatus in [130,140,143,137,104,134,139] ? 'retry' : 'finish' }
process.maxRetries = 3
params.max_cpus = 8
params.element_annotations_samplesheet = "/oak/stanford/groups/horence/kaitlin/bowtie2_annotations/references/bowtie2_index_samplesheet.csv"
params.genome_index = "/oak/stanford/groups/horence/kaitlin/bowtie2_annotations/references/base_references/grch38_1kgmaj/grch38_1kgmaj"
params.transcriptome_index = "/oak/stanford/groups/horence/circularRNApipeline_Cluster/index/GRCh38.gencode.v31_transcriptome"
params.gene_bed = "/oak/stanford/groups/horence/kaitlin/annotation_beds/cleaned_hg38_genes.bed"
params.star_index = "/oak/stanford/groups/horence/Roozbeh/single_cell_project/SICILIAN_references/human/SICILIAN_human_hg38_Refs/star_ref_file/hg38_ERCC_STAR_2.7.5.a"
params.gtf = "/oak/stanford/groups/horence/Roozbeh/single_cell_project/SICILIAN_references/human/SICILIAN_human_hg38_Refs/gtf_file/grch38_known_genes.gtf"
}
sherlock {
process.executor = 'slurm'
process.clusterOptions = '-p owners,normal --requeue'
process.queueSize = 500
process.pollInterval = '3 min'
process.dumpInterval = '6 min'
process.queueStatInterval = '5 min'
process.exitReadTimeout = '13 min'
process.submitRateLimit = '5sec'
process.memory = { 20.GB * task.attempt }
process.time = { 1.h * task.attempt }
process.errorStrategy = { task.exitStatus in [130,140,143,137,104,134,139] ? 'retry' : 'finish' }
process.maxRetries = 3
params.max_cpus = 8
}
horence_quake {
process.executor = 'slurm'
process.clusterOptions = '-p horence,quake --requeue'
process.queueSize = 500
process.pollInterval = '3 min'
process.dumpInterval = '6 min'
process.queueStatInterval = '5 min'
process.exitReadTimeout = '13 min'
process.submitRateLimit = '5sec'
process.memory = { 20.GB * task.attempt }
process.time = { 1.h * task.attempt }
process.errorStrategy = { task.exitStatus in [130,140,143,137,104,134,139] ? 'retry' : 'finish' }
process.maxRetries = 3
params.max_cpus = 8
params.element_annotations_samplesheet = "/oak/stanford/groups/horence/kaitlin/bowtie2_annotations/references/bowtie2_index_samplesheet.csv"
params.genome_index = "/oak/stanford/groups/horence/kaitlin/bowtie2_annotations/references/base_references/grch38_1kgmaj/grch38_1kgmaj"
params.transcriptome_index = "/oak/stanford/groups/horence/circularRNApipeline_Cluster/index/GRCh38.gencode.v31_transcriptome"
params.gene_bed = "/oak/stanford/groups/horence/kaitlin/annotation_beds/cleaned_hg38_genes.bed"
params.star_index = "/oak/stanford/groups/horence/Roozbeh/single_cell_project/SICILIAN_references/human/SICILIAN_human_hg38_Refs/star_ref_file/hg38_ERCC_STAR_2.7.5.a"
params.gtf = "/oak/stanford/groups/horence/Roozbeh/single_cell_project/SICILIAN_references/human/SICILIAN_human_hg38_Refs/gtf_file/grch38_known_genes.gtf"
}
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
process.container = 'kaitlinchaung/nomad:v0.1'
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
process.container = 'kaitlinchaung/nomad:v0.1'
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag.svg"
}
manifest {
name = 'kaitlinchaung/nomad'
author = 'Kaitlin Chaung'
homePage = 'https://github.com/kaitlinchaung/nomad'
description = 'pass'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '1.0dev'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${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
}
}
}