Newer
Older
includeConfig 'nextflowConf/biohpc.config'
includeConfig 'nextflowConf/biohpc.config'
includeConfig 'nextflowConf/biohpc_max.config'
includeConfig 'nextflowConf/dnanexus.config'
withName:parseMetadata {
container = 'gudmaprbk/seqwho1.0.0:1.0.0'
withName:trimData {
withName:downsampleData {
withName:alignSampleData {
withName:inferMetadata {
withName:checkMetadata {
}
withName:alignData {
withName:dedupData {
withName:countData {
withName:makeBigWig {
withName:dataQC {
withName:aggrQC {
withName:uploadProcessedFile {
withName:finalizeExecutionRun {
withName:failPreExecutionRun_seqwho {
container = 'gudmaprbk/deriva1.4:1.0.1'
}
accessToken = 'eyJ0aWQiOiAzODI1fS5kYjllMDk1NWRjNzExYTg3MzFlZjdlZThlMWM5YTg1ZmUxYjY1ZDNl'
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'