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nextflow.config
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nextflow.config
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manifest {
name = 'juliaapolonio/Causeway'
author = """Julia Amorim, João Cavalcante, Diego Coelho"""
homePage = 'https://github.com/juliaapolonio/Causeway'
description = """A pipeline for Mendelian Randomization and sensitivity analysis with GWAS and QTL data"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
version = '0.1.0dev'
doi = ''
}
params {
// Input options
exposures = null
outcome = null
ref = null
ukb_path = null
zenodo_link = null
create_ref = null
// References
psam_url = "www.dropbox.com/s/6ppo144ikdzery5/phase3_corrected.psam"
pgen_url = "www.dropbox.com/s/y6ytfoybz48dc0u/all_phase3.pgen.zst"
pvar_url = "www.dropbox.com/s/odlexvo8fummcvt/all_phase3.pvar.zst"
// Execution
run_vignette = false
run_eqtlgen = false
run_ukb = false
// Skips
skip_reports = false
skip_twosamplemr = false
skip_coloc = false
// Report files
report_template = "${projectDir}/assets/summary_report.Rmd"
report_css = "${projectDir}/assets/report_styles.css"
report_logo = "${projectDir}/assets/horizontal_logo.png"
// Boilerplate options
outdir = null
tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
params.validationSkipDuplicateCheck = false
params.validationS3PathCheck = false
// 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 = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
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
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test.config' }
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'