Can someone explain to me why doing this:

ch_main_assembled
        .branch {
            it ->
            polish:     ["pilon","medaka","medaka+pilon","dorado","dorado+pilon"].contains(it.meta.polish)
            no_polish: !["pilon","medaka","medaka+pilon","dorado","dorado+pilon"].contains(it.meta.polish)
        }
        .set { ch_main_assembled }

    ch_main_assembled.polish.view {"ch_main_assembled.polish: $it"}
    ch_main_assembled.no_polish.view {"ch_main_assembled.no_polish: $it"}

gives me this item in

no_polish

:

ch_main_assembled.no_polish: [meta:[id:test_flye_hifiasm, group:null, strategy:scaffold, assembler:flye_hifiasm, assembler_ont:flye, assembler_hifi:hifiasm, assembly_scaffolding_order:ont_on_hifi, assembler_ont_args:, assembler_hifi_args:, polish:"medaka+pilon" <extra items removed>]]

That's annoying, how did you read in the samplesheet? I think lots of programs will normally output cells in quotes to stop data being incorrectly split if using csv. But I thought most readers will handle the quotes?

I read the samplesheet with

channel.fromPath.splitCsv()

. I think the behaviour is actually fine, but it is not immediately obvious that

[polish:"medaka+pilon"]

is not contained in

["pilon","medaka","medaka+pilon","dorado","dorado+pilon"]

, I could have noticed the quotes though..