Channel Structure for Process with Grouped Files and Nested Lists

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1

I’m working on a Nanopore pipeline and need help with a complex channel definition in Nextflow. The goal is to create a channel that groups NanoStats.txt files from NanoPlot by order and sample, and then passes this structured data to an ENDPOINT_QC for further analysis.

Here’s my channel definition:

// Current workflow channel construction
    ch_endpoint_qc_groups = NANOPLOT.out.txt
        .map { meta, txt_files -> 
            // Extract order and sample from meta.id which is in format <order>_<sample>_<pod5>
            def (order, sample) = meta.id.split('_')[0..1]
            tuple(order, sample, txt_files)
        }
        .groupTuple(by: [0,1])  // Group by order and sample
        .map { order, sample, txt_files ->
            tuple(
                tuple(order, sample),  // Group
                txt_files.flatten()    // NanoStats.txt files
            )
        }
        .toList()
    // Then combine with samplesheet info using combine operator
    ch_endpoint_qc = ch_input_samplesheet
        .map { meta, sheet -> meta.id }
        .combine(ch_endpoint_qc_groups)

The channel looks like this:

[samplesheet_id, 
    [order1, sample1, [stats_file1, stats_file2, ...]],
    [order1, sample2, [stats_file3, stats_file4, ...]],
    [order2, sample1, [stats_file5, stats_file5, ...]],
     ...]

I need to ensure that the ENDPOINT_QC process can accept this structure and correctly parse it: the samplesheet, orders, and samples will be used as values, and the stats files are paths. But every input definition I try results in a warning about the input structure not matching the expected format. How should I define the input for the ENDPOINT_QC process to correctly handle this structure?

2

Great question Josh.

You’ll need to separate our paths from your metadata. Given your channel, which I’ll call joshChannel, you can use a map operator to separate out the metadata (and give them nice named keys) from the files:

joshChannel
| map { samplesheet, remainder -> 
    def (orders, samples, statsfiles) = remainder.transpose()
    [samplesheet, orders, samples, statsfiles]
}

Which will give you a channel like

[
    samplesheet.csv, 
    [order2, order2, order1, order1], 
    [sample2, sample1, sample2, sample1], 
    [
        [o2_s2_statsfile_1, o2_s2_statsfile_2.txt, o2_s2_statsfile_3.txt], 
        [o2_s1_statsfile_1, o2_s1_statsfile_3.txt, o2_s1_statsfile_2.txt], 
        [o1_s2_statsfile_3, o1_s2_statsfile_2.txt, o1_s2_statsfile_1.txt], 
        [o1_s1_statsfile_2, o1_s1_statsfile_3.txt, o1_s1_statsfile_1.txt]
    ]
]

which you can pass into a process like:

process ENDPOINT_QC {
    input: 
        path(samplesheet), path(orders), path(samples), path(statsfiles)
    // ... 
}

Would that fit your needs?