What kind of variable is created from subMap and branch

Nextflow Help
1

Hi Developers,

I’m using following code to read in some data (attached)

workflow {

Channel.fromPath("long_format_data.csv")
        .splitCsv(header: true).map { it ->
            [
                it.subMap("batch", "timepoint", "tissue", "sequencing_type"),
                [
                    file(it.fastq_1),
                    file(it.fastq_2)
                ]
            ]
        }
        .branch { meta, fastq ->
            rna: meta.tissue == "rna" && meta.sequencing_type == "rna"
            germline: meta.tissue == "normal" && meta.sequencing_type == "wes"
            tumor: meta.tissue == "tumor" && meta.sequencing_type == "wes"
            other: true
        }
        .set { input_ch }

//input_ch.germline| dump{tag: 'analysis', pretty: true}

input_ch.germline.view()
    
}

It prints following as expected I guess:

[[batch:SEMA-MM-001, timepoint:MM-3309-T-01, tissue:normal, sequencing_type:wes], [/data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-3309-DNA-N-01-01_L001_R1_001.fastq.gz, /data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-3309-DNA-N-01-01_L001_R2_001.fastq.gz]]

[[batch:SEMA-MM-001, timepoint:MM-0489-T-01, tissue:normal, sequencing_type:wes], [/data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0489-DNA-N-01-01_L001_R1_001.fastq.gz, /data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0489-DNA-N-01-01_L001_R2_001.fastq.gz]]

[[batch:SEMA-MM-001, timepoint:MM-0487-T-01, tissue:normal, sequencing_type:wes], [/data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0487-DNA-N-01-01_L001_R1_001.fastq.gz, /data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0487-DNA-N-01-01_L001_R2_001.fastq.gz]]

[[batch:SEMA-MM-001, timepoint:MM-0486-T-01, tissue:normal, sequencing_type:wes], [/data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0486-DNA-N-01-01_L001_R1_001.fastq.gz, /data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0486-DNA-N-01-01_L001_R2_001.fastq.gz]]

[[batch:SEMA-MM-001, timepoint:MM-0256-T-02, tissue:normal, sequencing_type:wes], [/data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0256-DNA-N-01-01_L001_R1_001.fastq.gz, /data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0256-DNA-N-01-01_L001_R2_001.fastq.gz]]

[[batch:SEMA-MM-001, timepoint:MM-0364-T-02, tissue:normal, sequencing_type:wes], [/data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0364-DNA-N-01-01_L001_R1_001.fastq.gz, /data1/raw_data/WES/sema4/SEMA-MM-001DNA/MM-0364-DNA-N-01-01_L001_R2_001.fastq.gz]]

I’m new to the world of groovy, nextflow thus I’m having some difficulty.

What kind of variable is input_ch? Is it a list or a multi-channel or an array or
something else?

Please help me to understand the variable.
Thanks
long_format_data.csv (11.8 KB)

2

Hey, @complexgenome.

input_ch is a Nextflow multi-channel variable. input_ch.germline is a Nextflow channel.

3

@mribeirodantas Thank you for your reply.

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