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nextflow.config
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nextflow.config
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//Main config file for PerCell pipeline
process {
// Global process config
executor = 'slurm'
withLabel: process_low {
cpus = 2
}
withLabel: process_medium {
cpus = 6
}
withLabel: process_high {
cpus = 8
}
withLabel: process_long {
time = 20.h
}
withLabel: process_high_memory {
clusterOptions = '--partition=himem'
cpus = 4
}
}
params {
max_memory = 1000.GB
max_cpus = 10
max_time = 120.h
// input/output default params
input = 'example/example_input.csv'
outdir = 'PerCell_Output'
aligner = 'bowtie2'
experimental = 'human'
spikein = 'mouse'
seq_center = ''
enable_conda = ''
// reference genome fastas and blacklists, replace with paths to downloaded reference genomes as required
human_fa = ''
mouse_fa = ''
zebrafish_fa = ''
fly_fa = ''
human_blacklist = "$projectDir/assets/hg38-blacklist.v2.bed.gz"
mouse_blacklist = "$projectDir/assets/mm10-blacklist.v2.Liftover.mm39.bed.gz"
zebrafish_blacklist = "$projectDir/assets/blank_blacklist.bed.gz"
fly_blacklist = "$projectDir/assets/dm6-blacklist.v2.bed.gz"
// params for trimgalore
clip_r1 = 0
clip_r2 = 0
three_prime_clip_r1 = 0
three_prime_clip_r2 = 0
// indices, null as default but can be replaced with paths to skip index generation steps
human_chro_index = null
mouse_chro_index = null
zebrafish_chro_index = null
fly_chro_index = null
human_bowtie2_index = null
mouse_bowtie2_index = null
zebrafish_bowtie2_index = null
fly_bowtie2_index = null
// params for skipping specific processes
skip_fastqc = true
skip_trimming = true
save_trimmed = false
override_spikeinfail = false
skip_downsample = false
skip_annotation = true
skip_motif = true
// genome sizes needed for MACS2
macs_gsize_human = 2700000000
macs_gsize_mouse = 1870000000
macs_gsize_zebrafish = 1679203469
macs_gsize_fly = 120000000
// Replace with paths to downloaded annotation files as required
human_gtf = ''
mouse_gtf = ''
zebrafish_gtf = ''
fly_gtf = ''
// seed for randomizing downsampling
seed = ''
// params for peak calling and bigWig generation
min_reps_consensus = 1
narrow_peak = true
broad_cutoff = 0.1
macs2_cutoff = 1.301
macs2_peak_method = 'ppois'
macs2_bigwig_method = 'ppois'
skip_idr = true
idr_cutoff = 0.05
skip_consensus = true
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// reset from main.nf to PC.nf
manifest.mainScript = 'PC.nf'
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}