Revision 42a79999f11304671b9d22e4959b0167b2130944 authored by Thanh LĂȘ on 06 April 2020, 09:49:06 UTC, committed by GitHub on 06 April 2020, 09:49:06 UTC
pin ivar to 1.2
1 parent f0ba0a1
illuminaNcov.nf
#!/usr/bin/env nextflow
// enable dsl2
nextflow.preview.dsl = 2
// import modules
include {articDownloadScheme } from '../modules/artic.nf'
include {makeIvarBedfile} from '../modules/illumina.nf'
include {readTrimming} from '../modules/illumina.nf'
include {readMapping} from '../modules/illumina.nf'
include {trimPrimerSequences} from '../modules/illumina.nf'
include {callVariants} from '../modules/illumina.nf'
include {makeConsensus} from '../modules/illumina.nf'
include {makeQCCSV} from '../modules/qc.nf'
include {writeQCSummaryCSV} from '../modules/qc.nf'
include {collateSamples} from '../modules/upload.nf'
// import subworkflows
include {CLIMBrsync} from './upload.nf'
workflow sequenceAnalysis {
take:
ch_filePairs
main:
articDownloadScheme()
readTrimming(ch_filePairs)
readMapping(articDownloadScheme.out.scheme.combine(readTrimming.out))
trimPrimerSequences(articDownloadScheme.out.bed.combine(readMapping.out))
callVariants(trimPrimerSequences.out.ptrim.combine(articDownloadScheme.out.reffasta))
makeConsensus(trimPrimerSequences.out.ptrim)
makeQCCSV(trimPrimerSequences.out.ptrim.join(makeConsensus.out, by: 0)
.combine(articDownloadScheme.out.reffasta))
makeQCCSV.out.csv.splitCsv()
.unique()
.branch {
header: it[-1] == 'qc_pass'
fail: it[-1] == 'FALSE'
pass: it[-1] == 'TRUE'
}
.set { qc }
writeQCSummaryCSV(qc.header.concat(qc.pass).concat(qc.fail).toList())
collateSamples(qc.pass.map{ it[0] }
.join(makeConsensus.out, by: 0)
.join(trimPrimerSequences.out.mapped))
emit:
qc_pass = collateSamples.out
}
workflow ncovIllumina {
take:
ch_filePairs
main:
sequenceAnalysis(ch_filePairs)
if ( params.upload ) {
Channel.fromPath("${params.CLIMBkey}")
.set{ ch_CLIMBkey }
CLIMBrsync(sequenceAnalysis.out.qc_pass, ch_CLIMBkey )
}
}
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