How to access attributes from subMap and branch to print

[complexgenome (S)]

Hi developers,

I’m interested to print attributes created by subMap but so far I’ve not been able to make much success.

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.view()
    
}

I’d like to print say input_ch.germline.tumor or input_ch.germline.batch or input_ch.germline.tissue

How do I achieve it?

[mribeirodantas (Marcel Ribeiro-Dantas)]

You can use closures with operators to achieve that. If you want to print to the screen, you can do with:

  ...

   input_ch.germline.view { it -> it[0]['batch'] }
}

This is your first channel element:

[
  [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-MM001DNA/MM-3309-DNA-N-01-01_L001_R2_001.fastq.gz]
]

This is the first item (it[0]):

[
  batch:SEMA-MM-001,
  timepoint:MM-3309-T-01,
  tissue:normal,
  sequencing_type:wes
]

And this is it[0]['batch']:

SEMA-MM-001

Output:

Instead of viewing them all, you could want to see only the channel elements whose batch value equals SEMA-MM-003. Then you’d do:

  ...

  input_ch.germline.filter { it[0]['batch'] == 'SEMA-MM-003' }.view()
}

Output:

PS: No need to use the -dump-channels option here. I was answering your other question so I kept using it out of habit

[complexgenome (S)]

@mribeirodantas
Thank you, it works and helps.

How about printing batch timepoint or tissue together?

input_ch.germline.view { it -> it[0]['batch'], it[0]['tissue']   }

I used following code it failed with error of

ERROR ~ Unknown method invocation call on LinkedHashMap type

long_format_data.csv (11.8 KB)

[mribeirodantas (Marcel Ribeiro-Dantas)]

@complexgenome

input_ch.germline.view { it -> it[0]['batch'], it[0]['tissue']   }

You need to encapsulate it within brackets. See the corrected snippet below:

input_ch.germline.view { it -> [it[0]['batch'], it[0]['tissue']]  }