I am trying to write a nextflow script below:
/*
* pipeline input parameters
*/
params.reads = "/path/to/fq/files/"
params.guide_library = "/path/to/guidelibrary/"
params.outdir = "results"
log.info """
DUAL GUIDE CRISPR QC - N F P I P E L I N E
===================================
guide library: ${params.guide_library}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent(true)
/*
- define the
index process that creates a binary index
- given the transcriptome file
*/
process READCOUNT {
input:
path guide_library
tuple val(sample_name) path(reads)
output:
path "$sample_name"
script:
"""
exactcounts.py -inputlibrary <span class="math-container">$guide_library -read1 $</span>{reads[0]} -read2 <span class="math-container">${reads[1]} -prefix $</span>sample_name
"""
}
workflow {
Channel
.fromFilePairs(params.reads, checkIfExists: true)
.set { read_pairs_ch }
count_ch = READCOUNT(params.guide_library,read_pairs_ch)
}
But am getting the following error:
Process 'READCOUNT' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context
