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I'm new to nextflow, channel, process. Kindly bear with me. I'd like to create a pipeline, pass paired reads from one to another process. I am unable to do it.
script1.nf
params.outdir = 'results'
params.reads1 = "/Users/user/Downloads/tiny/normal/*_R1_xxx.fastq.gz"
params.reads2 = "/Users/user/Downloads/tiny/normal/*_R2_xxx.fastq.gz"
println "reads: $params.reads1"
println "reads: $params.reads2"
Channel.fromPath(params.reads1,checkIfExists: true).view()
Channel.fromPath(params.reads2,checkIfExists: true).view()
include { fastp } from '/Users/name/Documents/name/nextflow_scripts/fastp.nf'
fqpairs_ch=channel.fromFilePairs('/Users/name/Downloads/tiny/normal/*_R{1,2}_xxx.fastq.gz')
process check {
output:
stdout
"""
echo "hello from command line \n"
"""
}
workflow {
check().view(). /// this works
fastp(fqpairs_ch).view() // it gives error
}
fastp.nf
params.outdir = "./results"
process fastp() {
tag "fastp on $sample_id"
input:
tuple val(sample_id), file(x), file(x1) from fqpairs_ch
output:
println ("$sample_id")
script:
"""
mkdir fastp_trimmed
fastp \
--correction \
--cut_tail \
--disable_trim_poly_g \
--length_required 50 \
--qualified_quality_phred 20 \
--thread 12 \
--trim_poly_x \
--unqualified_percent_limit 20 \
-i ${x[0]} -I ${x[1]} \
-o fastp_trimmed/joinedfiles.dat_${x[0]} -O fastp_trimmed/joinedfiles.dat_${x[1]}
"""
}
Error:
ERROR ~ No such variable: fqpairs_ch
-- Check script 'fastp.nf' at line: 13 or see '.nextflow.log' file for more details
I'm unable to wrap by head around tag, val. Also, it is difficult for me to understand how to pass variable from one script to another. I've watched Youtube tutorial but with limited success.
