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nextflow.config
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nextflow.config
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aws {
region = 'ap-southeast-1'
client {
maxConnections = 10
connectionTimeout = 10000
storageEncryption = 'AES256'
}
}
// process {
// executor = 'awsbatch'
// queue = 'arn:aws:batch:us-east-1:<account>:job-queue/<queue-name>'
// errorStrategy = 'terminate'
// aws.batch.cliPath = '/usr/local/bin/aws'
// container = 'sentieon/sentieon-aws:201911-3'
// }
docker {
enabled = true
container = 'nfcore/sentieon'
// docker.runOptions='-u $(id -u):$(id -g)'
temp = 'auto'
envWhitelist = "SENTIEON_LICENSE"
}
params {
input = "nextflow_input.csv"
ref = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa"
ref_fai = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa.fai"
ref_amb = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa.amb"
ref_ann = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa.ann"
ref_bwt = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa.bwt"
ref_pac = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa.pac"
ref_sa = "s3://flowcelltest/None/sentieon-genomics-directory/reference/hg38.fa.sa"
ref_dict = "s3://flowcelltest/None/sentieon-genomics-directory/reference/reference.dict"
fastqr1 = "s3://flowcelltest/None/sentieon-genomics-directory/sentieon-splitfastq-files/10591_1.part_001.fq.gz"
fastqr2 = "s3://flowcelltest/None/sentieon-genomics-directory/sentieon-splitfastq-files/10591_2.part_001.fq.gz"
sample_id = "10591_s3_9"
SENTIEON_INSTALL_DIR = "/home/ubuntu/sentieon/sentieon-genomics-202112.01"
ref_mills = "s3://flowcelltest/None/sentieon-genomics-directory/reference/Mills_and_1000G_gold_standard.indels.hg38.vcf"
ref_mills_tbi = "s3://flowcelltest/None/sentieon-genomics-directory/reference/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi"
ref_mill_idx = "s3://flowcelltest/None/sentieon-genomics-directory/reference/Mills_and_1000G_gold_standard.indels.hg38.vcf.idx"
ref_dbsnp = "s3://flowcelltest/None/sentieon-genomics-directory/reference/common_all_20180418.vcf"
ref_dbsnp_idx = "s3://flowcelltest/None/sentieon-genomics-directory/reference/common_all_20180418.vcf.idx"
// wes_bedfile = "/home/ubuntu/sentieon/sentieon-genomics-202112.01/output"
threads = 16
chunk_size = 10000000
output_dir = "s3://flowcelltest/None/sentieon-genomics-directory/sentieon-splitfastq-files/output/"
outpath = "s3://flowcelltest/None/sentieon-genomics-directory/sentieon-splitfastq-files/output/"
script_dir = "/tmp"
code_ver = "2022.06.01"
aws_region = "ap-southeast-1"
wes = false
}
params.outdir='/home/ec2-user/nextflow/outputs'
env.SENTIEON_LICENSE = '172.31.27.7:8990'