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Process per CSV record


You need to execute a task for each record in one or more CSV files.


Read the CSV file line-by-line using the splitCsv operator, then use the map operator to return a tuple with the required field for each line and convert any string path to a file path object using the file function. Finally, use the resulting channel as input for the process.


Given the file index.csv with the following content:

sampleId read1 read2
FC816RLABXX reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_1.fq.gz reads/110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_2.fq.gz
FC812MWABXX reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz reads/110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_2.fq.gz
FC81DE8ABXX reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_1.fq.gz reads/110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_2.fq.gz
FC81DB5ABXX reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz reads/110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz
FC819P0ABXX reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_1.fq.gz reads/110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_2.fq.gz

This workflow parses the file and executes a process for each line:

params.index = "$baseDir/data/index.csv"

process foo {
    debug true
    tuple val(sampleId), file(read1), file(read2)

    echo your_command --sample $sampleId --reads $read1 $read2

workflow {
    Channel.fromPath(params.index) \
        | splitCsv(header:true) \
        | map { row-> tuple(row.sampleId, file(row.read1), file(row.read2)) } \
        | foo


Relative paths are resolved by the file function against the execution directory. In practice, it is preferable to use absolute file paths.

Run it

Use the the following command to execute the example:

nextflow run nextflow-io/patterns/