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nextflow.config
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params {
ref = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
dbsnp = 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz'
dbsnp_index = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
fasta_index = [
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict",
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
]
bwa_index = [
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.alt",
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.amb",
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.ann",
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.bwt",
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.pac",
"s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/Homo_sapiens_assembly38.fasta.64.sa",
]
readgroups = "@RG\\tID:HG002-1\\tSM:HG002\\tLB:HG002-LB-1\\tPL:ILLUMINA"
model = 's3://pgpuk/pgp650/SentieonIlluminaWGS2.2.bundle'
output_dir = 'output'
}
profiles {
local {
process.executor = 'local'
}
}
process {
errorStrategy = 'terminate'
// errorStrategy = 'ignore'
}
docker {
enabled = true
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "results/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "results/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "results/pipeline_info/pipeline_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "results/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}