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Gervaise Henry authoredb08a7fc5
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nextflow.config 2.60 KiB
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profiles {
standard {
includeConfig 'conf/biohpc.config'
}
biohpc {
includeConfig 'conf/biohpc.config'
}
biohpc_max {
includeConfig 'conf/biohpc_max.config'
}
aws_ondemand {
includeConfig 'conf/aws.config'
includeConfig 'conf/ondemand.config'
}
aws_spot {
includeConfig 'conf/aws.config'
includeConfig 'conf/spot.config'
}
}
process {
withName:getBag {
container = 'bicf/gudmaprbkfilexfer:2.0.1_indev'
}
withName:getData {
container = 'bicf/gudmaprbkfilexfer:2.0.1_indev'
}
withName: parseMetadata {
container = 'gudmaprbk/python3:1.0.0'
}
withName: trimData {
container = 'bicf/trimgalore:1.1'
}
withName: getRefInfer {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName: downsampleData {
container = 'bicf/seqtk:2.0.1_indev'
}
withName: alignSampleData {
container = 'bicf/gudmaprbkaligner:2.0.1_indev'
}
withName: inferMetadata {
container = 'bicf/rseqc3.0:2.0.1_indev'
}
withName: getRef {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName: alignData {
container = 'bicf/gudmaprbkaligner:2.0.1_indev'
}
withName: dedupData {
container = 'bicf/gudmaprbkdedup:2.0.0'
}
withName: countData {
container = 'bicf/subread2:2.0.0'
}
withName: makeBigWig {
container = 'bicf/deeptools3.3:2.0.1_indev'
}
withName: fastqc {
container = 'bicf/fastqc:2.0.1_indev'
}
withName: dataQC {
container = 'bicf/rseqc3.0:2.0.1_indev'
}
withName: aggrQC {
container = 'bicf/multiqc1.8:2.0.1_indev'
}
withName:uploadInputBag {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName:uploadExecutionRun {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName:uploadQC {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName:uploadProcessedFile {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
withName:uploadOutputBag {
container = 'gudmaprbk/deriva1.3:1.0.0'
}
}
trace {
enabled = false
file = 'pipeline_trace.txt'
fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
}
timeline {
enabled = false
file = 'timeline.html'
}
report {
enabled = false
file = 'report.html'
}
tower {
accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
enabled = true
}
manifest {
name = 'gudmap_rbk/rna-seq'
homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
mainScript = 'rna-seq.nf'
version = 'v0.0.4_indev'
nextflowVersion = '>=19.09.0'
}