Hello everyone, I'm trying to run nf-core/oncoanalyser using singularity offline for my CRAMs ultima files. I have setup everything needed including configs and when I run the pipeline, I keep getting error in REDUX. I have tried to fix this error by filtering out for paired reads but I have 0 paired reads and I believe the pipeline works for single end reads too? Can anyone please let me know how to navigate this when you can?? 002522.314 [Thread-49] [ERROR] read(id(413777_2-4215745261) coords(chr4:131253272-131253304) isPaired(false) cigar(110S33M75S) flags(2048)) exception: java.lang.IllegalStateException: Inappropriate call if not paired read java.lang.IllegalStateException: Inappropriate call if not paired read at htsjdk.samtools.SAMRecord.requireReadPaired(SAMRecord.java:892) at htsjdk.samtools.SAMRecord.getFirstOfPairFlag(SAMRecord.java:950) at com.hartwig.hmftools.redux.common.FragmentCoords.fromRead(FragmentCoords.java:231) at com.hartwig.hmftools.redux.ReadCache.processRead(ReadCache.java:67) at com.hartwig.hmftools.redux.PartitionReader.processSamRecord(PartitionReader.java:301) at com.hartwig.hmftools.redux.BamReader.sliceRegion(BamReader.java:82) at com.hartwig.hmftools.redux.PartitionReader.processRegion(PartitionReader.java:165) at com.hartwig.hmftools.redux.PartitionReader.processPartition(PartitionReader.java:119) at com.hartwig.hmftools.redux.PartitionThread.run(PartitionThread.java:59)

Very much one for the Hartwig team. Support for Ultima and SBX is on the roadmap for later this year, and there are versions of the various WiGiTS methods around that can handle Ultima data but I would not expect this to work with oncoanalyser for the time being,

I see! thanks

Adding in @Peter Priestley to see if this is a known issues or new. And yes as Oliver says, we're working hard on full cross platform compatibility this year but not quite there yet for 'out of the box' running