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nextflow.config
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manifest {
homePage = 'https://gitlab.labmed.uw.edu/genetics/umi_nextflow'
description = 'UMI pipeline written in nextflow.'
version = '0.1'
name = 'umi-nextflow'
}
profiles {
uw_batch {
params {
input_folder = 's3://uwlm-personal/nkrumm/umi/fastq/280R/'
run_id = "280R"
output = "s3://uwlm-personal/nkrumm/umi/out/"
// options
downsample_reads = null
save_intermediate_output = false
// reference files
picard_targets = "s3://uwlm-personal/nkrumm/umi/reference/MONC_estimated_targets.nochr.interval_list"
picard_baits = "s3://uwlm-personal/nkrumm/umi/reference/MONC_ctDNA1.3_designed_probe_coords_180314_no_chr.probes.interval_list"
bed = "s3://uwlm-personal/nkrumm/umi/reference/MONC_ctDNA1.3_designed_probe_coords_180314_no_chr.bed"
ref_fasta = "s3://uwlm-personal/nkrumm/references/hs37.fa"
ref_index = "s3://uwlm-personal/nkrumm/references/hs37.fa.{amb,ann,bwt,pac,sa,dict,fai}"
}
workDir = 's3://uwlm-nextflow-data/workdir/umi-nextflow'
process {
scratch = "/docker_scratch"
queue = 'ngs-queue'
executor = 'awsbatch'
withLabel:bwa {
container = 'nkrumm/alignment2'
cpus = 30
memory = "60GB"
}
withLabel:fgbio{
container = 'quay.io/biocontainers/fgbio:1.1.0--0'
}
withLabel:sambamba{
container = 'quay.io/biocontainers/sambamba:0.7.1--h148d290_2'
cpus = 8
memory = "12 GB"
}
withLabel:picard{
container = 'quay.io/biocontainers/picard:2.22.1--0'
}
withLabel:vardict{
container = 'quay.io/biocontainers/vardict:1.7.0--0'
}
withLabel:fastqc{
container = 'quay.io/biocontainers/fastqc:0.11.8--1'
}
withLabel:mosdepth{
container = 'quay.io/biocontainers/mosdepth:0.2.9--hbeb723e_0'
}
withLabel:multiqc{
container = 'nkrumm/multiqc-pandas:2e12cff'
}
}
aws {
region = 'us-west-2'
batch {
volumes = '/docker_scratch'
cliPath = '/home/ec2-user/miniconda/bin/aws'
}
}
}
local {
params {
// Input folder needs trailing slash
input_folder = '/mnt/disk10/users/sheenams/umi_nextflow/test/'
workDir = '/mnt/disk10/users/sheenams/umi_nextflow/'
output = 'output'
run_id = 'test'
// options
downsample_reads = null
save_intermediate_output = false
// reference files
picard_intervals = '/mnt/disk2/com/Genomes/Picard/MONC_ctDNA1.3_designed_probe_coords_180314_no_chr.Picard.bed'
ref_fasta = '/mnt/disk2/com/Genomes/gatk-bundle/human_g1k_v37.fasta'
ref_index = '/mnt/disk2/com/Genomes/gatk-bundle/human_g1k_v37.fasta.{amb,ann,bwt,pac,sa,dict,fai}'
bed = '/mnt/disk2/com/Genomes/BED_Files/MONC_ctDNA1.3_designed_probe_coords_180314_no_chr.bed'
}
process {
withLabel:bwa {
container = 'nkrumm/alignment2'
cpus = 8
memory = "30GB"
}
withLabel:fgbio{
container = 'quay.io/biocontainers/fgbio:1.1.0--0'
}
withLabel:sambamba{
container = 'quay.io/biocontainers/sambamba:0.7.1--h148d290_2'
cpus = 8
memory = "12 GB"
}
withLabel:picard{
container = 'quay.io/biocontainers/picard:2.22.1--0'
}
withLabel:vardict{
container = 'quay.io/biocontainers/vardict:1.7.0--0'
}
withLabel:fastqc{
container = 'quay.io/biocontainers/fastqc:0.11.8--1'
}
withLabel:mosdepth{
container = 'quay.io/biocontainers/mosdepth:0.2.9--hbeb723e_0'
}
withLabel:multiqc{
container = 'nkrumm/multiqc-pandas:2e12cff'
}
}
aws {
region = 'us-west-2'
}
docker {
enabled = true
temp = 'auto'
}
}
docker_s3_local {
params {
input_folder = 's3://uwlm-personal/nkrumm/umi/fastq/280R/'
run_id = "280R"
output = "s3://uwlm-personal/nkrumm/umi/out/"
// options
downsample_reads = 1000000
save_intermediate_output = false
// reference files
picard_targets = "s3://uwlm-personal/nkrumm/umi/reference/MONC_estimated_targets.nochr.interval_list"
picard_baits = "s3://uwlm-personal/nkrumm/umi/reference/MONC_ctDNA1.3_designed_probe_coords_180314_no_chr.probes.interval_list"
bed = "s3://uwlm-personal/nkrumm/umi/reference/MONC_ctDNA1.3_designed_probe_coords_180314_no_chr.bed"
ref_fasta = "s3://uwlm-personal/nkrumm/references/hs37.fa"
ref_index = "s3://uwlm-personal/nkrumm/references/hs37.fa.{amb,ann,bwt,pac,sa,dict,fai}"
}
process {
withLabel:bwa {
container = 'nkrumm/alignment2'
cpus = 8
memory = "30GB"
}
withLabel:fgbio{
container = 'quay.io/biocontainers/fgbio:1.1.0--0'
}
withLabel:sambamba{
container = 'quay.io/biocontainers/sambamba:0.7.1--h148d290_2'
cpus = 8
memory = "12 GB"
}
withLabel:picard{
container = 'quay.io/biocontainers/picard:2.22.1--0'
}
withLabel:vardict{
container = 'quay.io/biocontainers/vardict:1.7.0--0'
}
withLabel:fastqc{
container = 'quay.io/biocontainers/fastqc:0.11.8--1'
}
withLabel:mosdepth{
container = 'quay.io/biocontainers/mosdepth:0.2.9--hbeb723e_0'
}
withLabel:multiqc{
container = 'nkrumm/multiqc-pandas:2e12cff'
}
}
aws {
region = 'us-west-2'
}
docker {
enabled = true
temp = 'auto'
}
}
}