Error in executing nextflow script

Question

[Srinka]

The workflow was given as -

workflow {

mapping(Channel.fromPath('TRIM.out', 'buildIndex.out'))

}

The process is written as -

process mapping {
input: path 'TRIM.out' path 'buildIndex.out'

"""
bowtie2 -x $buildIndex.out $TRIM.out -S accepted_hits.sam
"""
}

[barslmn]

Could you format your code as code block?

Answer 1

[Pierre Lindenbaum]

the process mapping taks as input TWO path while Channel.fromPath('TRIM.out', 'buildIndex.out') is a stream of data, each data contains ONE path.

you want something like:

mapping(file('TRIM.out'),file('buildIndex.out'))