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nextflow.config 3.03 KiB
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profiles {
standard {
includeConfig 'nextflowConf/biohpc.config'
}
biohpc {
includeConfig 'nextflowConf/biohpc.config'
}
biohpc_max {
includeConfig 'nextflowConf/biohpc_max.config'
}
dnanexus {
includeConfig 'nextflowConf/dnanexus.config'
}
aws {
includeConfig 'nextflowConf/aws.config'
}
}
process {
withName:trackStart {
container = 'gudmaprbk/gudmap-rbk_base:1.0.1'
}
withName:getBag {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:getData {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:parseMetadata {
container = 'gudmaprbk/python3:1.0.1'
}
withName:getRefERCC {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:getRef {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:fastqc {
container = 'gudmaprbk/fastqc0.11.9:1.0.1'
}
withName:seqwho {
container = 'gudmaprbk/seqwho1.0.0:1.0.0'
}
withName:trimData {
container = 'gudmaprbk/trimgalore0.6.6:1.0.0'
}
withName:downsampleData {
container = 'gudmaprbk/seqtk1.3:1.0.1'
}
withName:alignSampleDataERCC {
container = 'gudmaprbk/hisat2.2.1:1.0.1'
}
withName:alignSampleData {
container = 'gudmaprbk/hisat2.2.1:1.0.1'
}
withName:inferMetadata {
container = 'gudmaprbk/rseqc4.0.0:1.0.1'
}
withName:checkMetadata {
container = 'gudmaprbk/gudmap-rbk_base:1.0.1'
}
withName:alignData {
container = 'gudmaprbk/hisat2.2.1:1.0.1'
}
withName:dedupData {
container = 'gudmaprbk/picard2.25.0:1.0.0'
}
withName:countData {
container = 'gudmaprbk/subread2.0.1:1.0.1'
}
withName:makeBigWig {
container = 'gudmaprbk/deeptools3.5.0:1.0.1'
}
withName:dataQC {
container = 'gudmaprbk/rseqc4.0.0:1.0.1'
}
withName:aggrQC {
container = 'gudmaprbk/multiqc1.10:1.0.0'
}
withName:uploadInputBag {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadQC {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadProcessedFile {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadOutputBag {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:finalizeExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:failPreExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:failPreExecutionRun_seqwho {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:failExecutionRun {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
withName:uploadQC_fail {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
}
tower {
accessToken = 'eyJ0aWQiOiAzODIyfS42YWFjOWMwZDM4Mjc1NmY0MGJiY2QxNWRkOTZlYTU4MDlmY2NkZmRj'
workspaceId = '84512216752206'
enabled = false
}
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 = 'v2.0.1'
nextflowVersion = '>=20.01.0'
}