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nextflow.config.task
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nextflow.config.task
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//Daniel Stribling
//Renne Lab, University of Florida
//CnR-flow Configuration File
//
// Config syntax:
// This config file uses the syntax described here:
// https://www.nextflow.io/docs/latest/config.html
// Primarily, "//" acts as a comment and allows removal/deactivation of lines.
//
// Settings within scopes, Ex:
// params {
// setting = value
// ...
// }
// are equivalent to:
// params.setting = value"
//
// Configuration Hierarchy:
// Different Nextflow configuration files have the precedence order:
// task-dir > pipe-dir > user-default > pipe-default
//
// This configruation is (presumably) in the task directory:
// (after running "nextflow CnR-flow --mode initiate" )
// and will therefore superceed pipe-setup, user, and pipe hardcoded defaults.
// For more detail visit: https://www.nextflow.io/docs/latest/config.html
//
// This configuration only includes task-specific parameters and parameters
// designed to be modified at runtime. Other parameters are provided in the
// pipe configuration, at CnR-flow/nextflow.config. Parameters
// provided here will override system defaults.
//
// Process Settings (For use of PBS, SLURM, etc)
process {
// --Executor, see: https://www.nextflow.io/docs/latest/executor.html
//executor = 'slurm' // for running processes using SLURM (Default: 'local')
// Process Walltime, See https://www.nextflow.io/docs/latest/process.html#process-time
//time = '12h'
// Process CPUs, See https://www.nextflow.io/docs/latest/process.html#cpus
//cpus = 8
//
// Memory: See https://www.nextflow.io/docs/latest/process.html#process-memory
// Set Memory for specific task sizes (1n/2n/4n scheme recommended)
//withLabel: big_mem { memory = '16 GB' }
//withLabel: norm_mem { memory = '4 GB' }
//withLabel: small_mem { memory = '2 GB' }
// -*OR*- Set Memory for all processes
//memory = "16 GB"
ext.ph = null //Placeholder to prevent errors.
}
params {
// REQUIRED values to enter (all others should work as default):
// ref_fasta (or some other ref-mode/location)
// treat_fastqs (input paired-end fastq[.gz] file paths)
// [OR fastq_groups] (mutli-group input paired-end .fastq[.gz] file paths)
// Automatic alignment reference preparation/usage settings:
ref_mode = 'fasta' // Options: ['name', 'fasta', 'manual']
ref_fasta = '' // REQUIRED: Ex: '/path/to/my/reference.fasta[.gz]'
// Default Pre-Supplied Normalization library is Ecoli:
norm_ref_fasta = "${projectDir}/ref_dbs/GCF_000005845.2_ASM584v2_genomic.fna.gz"
// CnR-flow Input Files:
// Provided fastqs must be in glob pattern matching pairs.
// Example: ['./relpath/to/base*R{1,2}*.fastq']
// Example: ['/abs/path/to/other*R{1,2}*.fastq']
treat_fastqs = [] // REQUIRED, Single-group Treatment fastq Pattern
ctrl_fastqs = [] // Single-group Control fastq pattern
// Can specify multiple treat/control groups as Groovy mapping.
// Specified INSTEAD of treat_fasts/ctrl_fastqs parameters.
// Note: There should be only one control sample per group
// (after optional lane combination)
// Example:
// fastq_groups = [
// 'group_1_name': ['treat': 'relpath/to/treat1*R{1,2}*',
// 'ctrl': 'relpath/to/ctrl1*R{1,2}*'
// ],
// 'group_2_name': ['treat': ['relpath/to/g2_treat1*R{1,2}*',
// '/abs/path/to/g2_treat2*R{1,2}*'
// ],
// 'ctrl': 'relpath/to/g2_ctrl1*R{1,2}*'
// ]
// ]
//fastq_groups = []
// ------- Step-Specific Pipeline Paramaters --------
// Step Settings:
do_merge_lanes = true // Merge sample names differing only by lane-ID (Ex: L001, L002)
do_fastqc = true // Perform FastQC Analysis
do_trim = true // Trim tags using Trimmomatic
do_norm_spike = true // Normalize using aligment count to a spike-in reference
do_norm_cpm = false // Normalize using millions of reads per sample
do_make_bigwig = true // Create UCSC bigWig files from final alignments
// FastQC Settings:
fastqc_flags = ''
// Alignment Mode Options (params.use_aln_modes) :
// "all" : Use all reads
// "all_dedup" : Use all reads, and remove duplicates.
// "less_120" : Use trimmed reads <= 120 bp
// "less_120_dedup" : Use trimmed reads <= 120 bp and remove duplicates.
// (Multiple modes can be performed in parallel. Ex: ['all', 'less_120'])
use_aln_modes = ["all"] // Options: ["all", "all_dedup", "less_120", "less_120_dedup"]
// Peak Caller Options (params.peak_callers):
// "macs2" : Call Peaks with Macs2
// "seacr" : Call Peaks with SEACR
// (Multiple callers can be used in parallel. Ex: ['macs2', 'seacr'])
peak_callers = ['macs', 'seacr'] // Options: ['macs', 'seacr']
// Trimmomatic Trim Settings
// --Trimmomatic Adapter Path, Downloaded after "nextflow CnR-flow --mode initiate"
//trimmomatic_adapterpath = "${projectDir}/ref_dbs/trimmomatic_adapters/TruSeq3-PE-2.fa"
trimmomatic_adapter_mode = "ILLUMINACLIP:"
trimmomatic_adapter_params = ":2:15:4:4:true"
trimmomatic_settings = "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25"
trimmomatic_flags = "-phred33"
// Bowtie2 Alignment Settings
aln_ref_flags = "--local --very-sensitive-local --phred33 -I 10 -X 700 --dovetail --no-unal --no-mixed --no-discordant"
// Normalization Settings
aln_norm_flags = params.aln_ref_flags
norm_scale = 1000 // Arbitrary value for scaling of normalized counts.
norm_mode = 'adj' // Options: ['adj', 'all']
// CPM Normalization Settings
norm_cpm_scale = 1000 // Arbitrary value for scaling of normalized counts.
// Macs2 Settings
macs_qval = '0.01'
macs_flags = ''
// SEACR Settings
seacr_fdr_threshhold = "0.01"
seacr_norm_mode = "auto" // Options: "auto", "norm", "non"
seacr_call_stringent = true
seacr_call_relaxed = true
// ------- General Pipeline Output Paramaters --------
publish_files = 'default' // Options: ["minimal", "default", "all"]
publish_mode = 'copy' // Options: ["symlink", "copy"]
// Name trim guide: ( regex-based )
// ~/groovy-slashy-string/ ; "~" denotes groovy pattern type.
// ~/^/ matches beginning ; ~/$/ matches end
trim_name_prefix = '' // Example: ~/^myprefix./ removes "myprefix." prefix.
trim_name_suffix = '' // Example: ~/_mysuffix$/ removes "_mysuffix" suffix.
// Workflow Output Default Naming Scheme:
// Absolute paths for output:
out_dir = "${launchDir}/cnr_output"
refs_dir = "${launchDir}/cnr_references"
}