nf-apache-poi: a Nextflow Plugin to read Excel files

nf-apache-poi is a Nextflow plugin able to read Excel files and emit their content via a Channel

Example

include { fromExcel } from 'plugin/nf-apache-poi'

workflow{
    Channel.fromExcel("example.xlsx", [tab:'Sheet1'])
            | view
}

Factory

fromExcel

Read a tab of the Excel file and emits a List<Object> (or a Map) per each row with the column values. If some cell is a formula, the evaluated value is returned

First argument is the path to the Excel file as a String

Second, optional, argument is a map with diferent configurations:

tab

String/number

the name or the index of the tab. First tab if not provided

skip

number

skip first n rows. No skip by default

header

boolean

if true use first row as keys for a map. False by default