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nextflow.config
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// Global default params, used in configs
params {
// Workflow flags
outdir = './results'
// Boilerplate options
help = false
tracedir = "${params.outdir}/pipeline_info"
// cache option makes it a bit easier to set conda or singularity cacheDir
cache = ''
// varCaller
varCaller = 'iVar'
viridian = false
analysis = false
// krakenDB
krakdb = '/data/databases/kraken2/minikraken2_v2_8GB_201904_UPDATE'
// GFF
GFF=false
gff=false
// upload bucket
uploadBucket=false
bucketNameFN4 = 'FN4-queue'
// primers
primers='auto'
//primers = 'https://raw.githubusercontent.com/iqbal-lab-org/viridian_workflow/master/viridian_workflow/amplicon_scheme_data/covid-artic-v3.vwf.tsv'
// parallel processing operation limit
myQueueSize = 100000
// number of maximum retries for errored processes
myMaxRetries = 5
// total number of error allowed per job
myMaxErrors = 1000
// process fork limit
myMaxForks = false
// execution UUID
run_uuid = 'no_uuid'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
if (params.varCaller == 'medaka'){
params.medaka=true
}
else if (params.varCaller == 'viridian'){
params.viridian=true
}
if ( params.medaka || params.nanopolish || params.viridian ){
includeConfig 'conf/nanopore.config'
}
if ( params.illumina ){
includeConfig 'conf/illumina.config'
if (params.varCaller == 'iVar'){
params.viridian=false
}
}
executor{
queueSize = params.myQueueSize
submitRateLimit = '5sec'
pollInterval = '15 sec'
}
profiles {
sp3 {
process {
scratch = true
errorStrategy = 'ignore'
}
report {
enabled = true
}
timeline {
enabled = true
}
dag {
enabled = true
}
trace {
enabled = true
}
}
conda {
if ( params.medaka || params.nanopolish ) {
process.conda = "$baseDir/environments/nanopore/environment.yml"
} else if (params.illumina) {
process.conda = "$baseDir/environments/illumina/environment.yml"
}
if (params.cache){
conda.cacheDir = params.cache
}
includeConfig 'conf/conda.config'
}
docker {
docker.enabled = true
fixOwnership = true
runOptions = "-u \$(id -u):\$(id -g)"
}
singularity {
process {
scratch = true
errorStrategy = 'ignore'
}
report {
enabled = true
}
timeline {
enabled = true
}
dag {
enabled = true
}
trace {
enabled = true
}
//singularity.enabled = true
singularity.autoMounts = true
if ( params.medaka || params.nanopolish || params.analysis ||(params.viridian && !params.illumina) ){
process {
withName:getObjCsv {
time = '30m'
singularity.enabled = true
container = '/data/images/oci_pipeline_v0.2.9.sif'
}
withName:articDownloadScheme {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-nanopore_v1.13.2.sif'
}
withName:articGuppyPlex {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-nanopore_v1.13.2.sif'
}
withName:articMinIONMedaka {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-nanopore_v1.13.2.sif'
}
withName:articRemoveUnmappedReads {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-nanopore_v1.13.2.sif'
}
withName:makeQCCSV {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-nanopore_v1.13.2.sif'
}
withName:writeQCSummaryCSV {
singularity.enabled = true
container = '/data/images/artic-ncov2019-nanopore_v1.13.2.sif'
}
withName:getObjFilesONT {
time = '30m'
singularity.enabled = true
container = '/data/images/oci_pipeline_v0.2.9.sif'
}
withName:pango {
time = '5m'
singularity.enabled = true
container = '/data/images/pango_v0.2.9.sif'
}
withName:nextclade {
time = '5m'
singularity.enabled = true
container = '/data/images/nextclade_v0.2.9.sif'
}
withName:download_nextclade_files {
time = '1h'
singularity.enabled = true
container = '/data/images/nextclade_v0.2.9.sif'
}
withName:getVariantDefinitions {
time = '1h'
singularity.enabled = true
container = '/data/images/aln2type_v0.2.9.sif'
}
withName:aln2type {
time = '5m'
singularity.enabled = true
container = '/data/images/aln2type_v0.2.9.sif'
}
withName:articMinIONViridian {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:viridianONTPrimers {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:viridianONTAuto {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:viridianPrimers {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:viridianAuto {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:FN4_upload {
time = '1h'
singularity.enabled = true
container = '/data/images/fn4_upload_v0.2.9.sif'
}
withName:uploadToBucket {
time = '1h'
singularity.enabled = true
container = '/data/images/fn4_upload_v0.2.9.sif'
}
withName:makeReport {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:getGFF3 {
time = '1h'
singularity.enabled = true
container = '/data/images/bcftools_v0.2.9.sif'
}
withName:bcftools_csq {
time = '1h'
singularity.enabled = true
container = '/data/images/bcftools_v0.2.9.sif'
}
}
} else if (params.illumina) {
process {
withName:getObjCsv {
time = '30m'
singularity.enabled = true
container = '/data/images/oci_pipeline_v0.2.9.sif'
}
withName:articDownloadScheme {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:indexReference {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:readTrimming {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:readMapping {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:trimPrimerSequences {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:callVariants {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:makeConsensus {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.21.sif'
}
withName:makeQCCSV {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:writeQCSummaryCSV {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:collateSamples {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:getObjFiles {
time = '30m'
singularity.enabled = true
container = '/data/images/oci_pipeline_v0.2.9.sif'
}
withName:pango {
time = '5m'
singularity.enabled = true
container = '/data/images/pango_v0.2.9.sif'
}
withName:nextclade {
time = '5m'
singularity.enabled = true
container = '/data/images/nextclade_v0.2.9.sif'
}
withName:download_nextclade_files {
time = '1h'
singularity.enabled = true
container = '/data/images/nextclade_v0.2.9.sif'
}
withName:getVariantDefinitions {
time = '1h'
singularity.enabled = true
container = '/data/images/aln2type_v0.2.9.sif'
}
withName:aln2type {
time = '5m'
singularity.enabled = true
container = '/data/images/aln2type_v0.2.9.sif'
}
withName:viridian {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:viridianPrimers {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:viridianAuto {
time = '45m'
singularity.enabled = true
container = '/data/images/viridian_workflow_v0.3.7.img'
}
withName:FN4_upload {
time = '1h'
singularity.enabled = true
container = '/data/images/fn4_upload_v0.2.9.sif'
}
withName:uploadToBucket {
time = '1h'
singularity.enabled = true
container = '/data/images/fn4_upload_v0.2.9.sif'
}
withName:makeReport {
time = '1h'
singularity.enabled = true
container = '/data/images/artic-ncov2019-illumina_v1.13.2.sif'
}
withName:getGFF3 {
time = '1h'
singularity.enabled = true
container = '/data/images/bcftools_v0.2.9.sif'
}
withName:bcftools_csq {
time = '1h'
singularity.enabled = true
container = '/data/images/bcftools_v0.2.9.sif'
}
}
}
if (params.cache) {
singularity.cacheDir = params.cache
}
}
oke {
process {
executor = 'k8s'
scratch = true
// Exponential backoff: 2s, 4s, 8s, 16s, 32s, and 1min thereafter.
errorStrategy = {
sleep(Math.max(60000, Math.pow(2, task.attempt) * 2000) as long)
return 'retry'
}
maxRetries = params.myMaxRetries
maxErrors = params.myMaxErrors
if (params.myMaxForks) {
maxForks = params.myMaxForks
}
}
k8s {
namespace = 'default'
storageClaimName = 'default-nextflow-fss-storage-work-pvc'
storageMountPath = '/work'
launchDir = "/work/runs/${params.run_uuid}"
serviceAccount = 'default'
projectDir = '/work/project'
pod = [
[label: 'pod-type', value: 'nextflow-worker'],
[volumeClaim: 'default-nextflow-fss-storage-data-pvc', mountPath: '/data'],
[imagePullSecret: 'sp3dockersecret'],
[imagePullPolicy: 'IfNotPresent']
]
}
report {
enabled = true
}
timeline {
enabled = true
}
dag {
enabled = true
}
trace {
enabled = true
}
if (params.medaka || params.nanopolish || params.analysis || (params.viridian && !params.illumina)){
process {
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/nf-head-pod:0c8df09c8e58'
withName:getObjCsv {
time = '30m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/oci_pipeline:v0.2.9'
}
withName:articDownloadScheme {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
withName:articGuppyPlex {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
withName:articMinIONMedaka {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
withName:articRemoveUnmappedReads {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
withName:makeQCCSV {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
withName:writeQCSummaryCSV {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
withName:getObjFilesONT {
time = '30m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/oci_pipeline:v0.2.9'
}
withName:pango {
time = '5m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/pango:v0.2.9'
}
withName:nextclade {
time = '5m'
container = 'lhr.ocir.io/lrbvkel2wjot/nextclade:1.11.0'
}
withName:download_nextclade_files {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/nextclade:1.11.0'
}
withName:getVariantDefinitions {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/aln2type:v0.2.9'
}
withName:aln2type {
time = '5m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/aln2type:v0.2.9'
}
withName:articMinIONViridian {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:viridianONTPrimers {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:viridianONTAuto {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:viridianPrimers {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:viridianAuto {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:FN4_upload {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/fn4_upload:v0.2.9'
}
withName:uploadToBucket {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/fn4_upload:v0.2.9'
}
withName:makeReport {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:getGFF3 {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/bcftools:v0.2.9'
}
withName:bcftools_csq {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/bcftools:v0.2.9'
}
withName:getWorkflowCommit {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
}
} else if (params.illumina) {
process {
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/nf-head-pod:0c8df09c8e58'
withName:getObjCsv {
time = '30m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/oci_pipeline:v0.2.9'
}
withName:articDownloadScheme {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:indexReference {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:readTrimming {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:readMapping {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:trimPrimerSequences {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:callVariants {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:makeConsensus {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:makeQCCSV {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:writeQCSummaryCSV {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:collateSamples {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:getObjFiles {
time = '30m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/oci_pipeline:v0.2.9'
}
withName:pango {
time = '5m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/pango:v0.2.9'
}
withName:nextclade {
time = '5m'
container = 'lhr.ocir.io/lrbvkel2wjot/nextclade:1.11.0'
}
withName:download_nextclade_files {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/nextclade:1.11.0'
}
withName:getVariantDefinitions {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/aln2type:v0.2.9'
}
withName:aln2type {
time = '5m'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/aln2type:v0.2.9'
}
withName:viridian {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:viridianPrimers {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:viridianAuto {
time = '45m'
container = 'lhr.ocir.io/lrbvkel2wjot/viridian_workflow:v0.3.7'
}
withName:FN4_upload {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/fn4_upload:v0.2.9'
}
withName:uploadToBucket {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/fn4_upload:v0.2.9'
}
withName:makeReport {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-illumina:v1.13.2'
}
withName:getGFF3 {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/bcftools:v0.2.9'
}
withName:bcftools_csq {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/bcftools:v0.2.9'
}
withName:getWorkflowCommit {
time = '1h'
container = 'lhr.ocir.io/lrbvkel2wjot/oxfordmmm/artic-ncov2019-nanopore:v1.13.2'
}
}
}
}
slurm {
process.executor = 'slurm'
}
lsf {
process.executor = 'lsf'
}
gls {
process.executor = 'google-lifesciences'
includeConfig 'conf/gls.config'
}
}
// COG-UK institutional config
includeConfig 'conf/coguk.config'
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
manifest {
author = 'Matt Bull'
description = 'Nextflow for running the Artic ncov2019 pipeline'
mainScript = 'main.nf'
nextflowVersion = '>=20.01.0'
version = 'sp3env-v0.2.9'
}