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nextflow.config
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nextflow.config
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// working directory for temporary/intermediate files produced in the workflow processes
workDir = "$HOME/temp"
params {
// Cybertron parameters for HPC
project = "207f23bf-acb6-4835-8bfe-142436acb58c"
queue = "sceaq"
// Define inputs and output directory
sample_sheet = './sample_sheets/test_sample_sheet.csv'
outdir = './results'
publish_dir_mode = 'copy'
// Genomic References
genome = 'GRCh38_no_alt' // required: value can be 'GRCh37-lite' or 'GRCh38_no_alt'
fasta_file = "/active/taylor_s/people/jsmi26/RPDEV/star_fusion_nf/resources/GRCh38/GRCh38_no_alt.fa"
gtf = "/active/taylor_s/people/jsmi26/RPDEV/star_fusion_nf/resources/GRCh38/gencode.v37.annotation.gtf.gz"
// STAR-aligner index
build_index = 'false' // required: boolean 'true' or 'false'
star_index_dir = '/active/taylor_s/people/jsmi26/RPDEV/star_fusion_nf/resources/GRCh38/reference/Homo_sapiens/GRCh38_no_alt/STAR_gencode_v37/GenomeDir' // required: filepath
// Fusion References
star_genome_lib = "/active/taylor_s/people/jsmi26/RPDEV/star_fusion_nf/resources/GRCh38/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir"
cicero_genome_lib = "/active/taylor_s/people/jsmi26/RPDEV/star_fusion_nf/resources/GRCh38/reference"
// Optionally, build fusion references
build_genome_library = 'false'
pfam_db = 'current'
dfam_db = 'human' // value of 'human', 'mouse', or filepath to Dfam.hmm database
}
// Execution variables used by tasks at runtime. Set TMPDIR to be scratch directory
env {
TMPDIR = "$HOME/temp"
}
// Computational resource allocation for the processes run in the workflow
process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
errorStrategy = "retry"
maxRetries = 1
//https://www.nextflow.io/docs/latest/process.html#scratch
scratch = false
// STAR process specific parameters
withName: STAR_PREP_FUSION {
ext.prefix = { "${sample}star." }
cpus = { 4 * task.attempt }
memory = { 32.GB * task.attempt }
ext.args = ''
}
// STAR process specific parameters
withName: STAR_FUSION {
ext.prefix = ''
cpus = { 4 * task.attempt }
memory = { 32.GB * task.attempt }
ext.args = { "--FusionInspector inspect --extract_fusion_reads --examine_coding_effect --verbose_level 2" }
}
// --misc_FI_opts '--out_prefix=${sample}'
withName: CICERO {
ext.prefix = { "${sample}${genome}" }
cpus = { 4 * task.attempt }
memory = { 32.GB * task.attempt }
ext.args = ''
}
withName: ARRIBA {
ext.prefix = ''
cpus = { 4 * task.attempt }
memory = { 32.GB * task.attempt }
ext.args = ''
}
withName: STAR_ALIGNER {
ext.prefix = { "${sample}cicero." }
cpus = { 2 * task.attempt }
memory = { 16.GB * task.attempt }
ext.args = ''
}
withName: STAR_INDEX {
ext.prefix = ''
publishDir = [ path: "${params.star_index_dir}",
mode: params.publish_dir_mode
]
cpus = { 2 * task.attempt }
memory = { 16.GB * task.attempt }
ext.args = ''
}
withName: BUILD_GENOME_REFS {
ext.prefix = ''
cpus = { 4 * task.attempt }
memory = { 64.GB * task.attempt }
ext.args = ''
}
withName: FASTQC {
ext.prefix = ''
cpus = { 1 * task.attempt }
memory = { 16.GB * task.attempt }
ext.args = ''
}
withName: MULTIQC {
ext.prefix = ''
cpus = { 1 * task.attempt }
memory = { 16.GB * task.attempt }
ext.args = '--export --data-dir --verbose'
}
withName: MD5SUMS {
ext.prefix = ''
cpus = 1
memory = { 16.GB * task.attempt }
ext.args = ''
}
withName: UNZIP {
ext.prefix = ''
cpus = 1
memory = { 8.GB * task.attempt }
ext.args = ''
}
}
//Create profiles to easily switch between the different process executors and platforms.
profiles {
//For executing the jobs on the HPC cluster with apptainer containers
PBS_apptainer {
process.executor = 'pbspro'
process.queue = "${params.queue}"
process.clusterOptions = "-P ${params.project}"
process.beforeScript = 'module load apptainer'
apptainer.enabled = true
}
//For running on cybertron with apptainer module loaded
local_apptainer {
process.executor = 'local'
apptainer.enabled = true
}
//For running on an interactive session on cybertron with singularity module loaded
local_singularity {
process.executor = 'local'
singularity.enabled = true
}
//For executing the jobs on the HPC cluster with singularity containers
PBS_singularity {
process.executor = 'pbspro'
process.queue = "${params.queue}"
process.clusterOptions = "-P ${params.project}"
process.beforeScript = 'module load singularity'
singularity.enabled = true
}
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
// https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/nextflow.config
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
//Configs for singularity containers on cybertron
singularity {
autoMounts = true
cacheDir = "$HOME/singularity"
runOptions = '--containall --no-home'
}
apptainer {
autoMounts = true
cacheDir = "$HOME/apptainer"
runOptions = '--containall --no-home'
}
//Use personal mamba/conda environments on cybertron if params.conda_enabled = true
conda {
cacheDir = "$HOME/mambaforge/envs/"
}
//overwrite reports when the workflow is executed again
report {
overwrite = true
}
dag {
overwrite = true
}