Commit 509bd3b0 authored by Raphael Müller's avatar Raphael Müller
Browse files

tenary operator indentation

parent a9597c30
......@@ -213,18 +213,19 @@ String BWAINDEX = "${output}/bwa_index"
if(bamAvailable){
chIlluminaBamMerge = (illuminaBamsAvailable) ? Channel.from(illuminaBamFiles).map{files -> files.split(fileSeparator)}.flatten().map{ file(it)} : Channel.empty()
chPacbioBamMerge = (pacbioBamsAvailable) ? Channel.from(pacbioBamFiles).map { files -> files.split(fileSeparator)}.flatten().map{file(it)} : Channel.empty()
chNanoporeBamMerge = (nanoporeBamsAvailable) ? Channel.from(nanoporeBamFiles).map { files -> files.split(fileSeparator)}.flatten().map{file(it)} : Channel.empty()
chIlluminaBamMerge = (illuminaBamsAvailable) ? Channel.from(illuminaBamFiles).map{files -> files.split(fileSeparator)}.flatten().map{file(it)} : Channel.empty()
chPacbioBamMerge = (pacbioBamsAvailable) ? Channel.from(pacbioBamFiles ).map{files -> files.split(fileSeparator)}.flatten().map{file(it)} : Channel.empty()
chNanoporeBamMerge = (nanoporeBamsAvailable) ? Channel.from(nanoporeBamFiles).map{files -> files.split(fileSeparator)}.flatten().map{file(it)} : Channel.empty()
}else if(assemblyAvailable){ //fi: bamAvailable
chBwaIndexGenome = (pairedAvailable || unpairedAvailable) ? Channel.fromPath(assembly) : Channel.empty()
chAssembly = Channel.fromPath(assembly).first()
chBwaIndexGenome = (pairedAvailable || unpairedAvailable) ? Channel.fromPath(assembly) : Channel.empty()
chUnpairedReadMapping = (unpairedAvailable) ? Channel.from(singleEnd).map{files -> files.split(fileSeparator)}.flatten().map{file it}.collate(1) : Channel.empty()
chPairedReadMapping = (pairedAvailable) ? Channel.from(pairedEnd).map{files -> files.split(fileSeparator)}.flatten().map{file it}.collate(2) : Channel.empty()
chPacbioReadMapping = (pacbioAvailable) ? Channel.from(pacbio).map { files -> files.split(fileSeparator)}.flatten().map{file it}.collate(1) : Channel.empty()
chNanoporeReadMapping = (nanoporeAvailable) ? Channel.from(nanopore).map { files -> files.split(fileSeparator)}.flatten().map{file it}.collate(1) : Channel.empty()
chAssembly = Channel.fromPath(assembly).first()
chPairedReadMapping = (pairedAvailable ) ? Channel.from(pairedEnd).map{files -> files.split(fileSeparator)}.flatten().map{file it}.collate(2) : Channel.empty()
chPacbioReadMapping = (pacbioAvailable ) ? Channel.from(pacbio ).map{files -> files.split(fileSeparator)}.flatten().map{file it}.collate(1) : Channel.empty()
chNanoporeReadMapping = (nanoporeAvailable) ? Channel.from(nanopore ).map{files -> files.split(fileSeparator)}.flatten().map{file it}.collate(1) : Channel.empty()
// Create index files for bwa mapping
process bwaIndexing {
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment