how to pass paired reads to another process in another script

[complexgenome]

Hi,
I am new to nextflow and this is difficult for me to understand for simple steps such as passing file pairs to another process in another script.
I have two scripts: 1) get paired reads 2) run fastp

one.nf

params.outdir = 'results'

params.reads1 = "/Users/name/Downloads/tiny/normal/*_R1_xxx.fastq.gz"
params.reads2 = "/Users/name/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/sariys01/Downloads/tiny/normal/*_R{1,2}_xxx.fastq.gz')

process check {

	output: 
	tuple val(fqpairs_ch)

	""" 
	echo "hello from command line \n"
	"""
}

workflow {

	check().view()
	fastp(fqpairs_ch).view()
}

fastp.nf

params.outdir = "./results"

process fastp() {

tag "$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

How do I capture the paired reads in fastp process defined in another script?

[complexgenome]

@bentsherman Can you please assist? I am new to nextflow and is complicated to understand.

[bentsherman]

Hi @sariya , you are mixing DSL1 and DSL2 syntax. In your fastp process, the from fqpairs_ch needs to be removed. Also, as a best practice you should put all of your channel logic in a workflow block. So the fqpairs_ch should be defined in your workflow block, and then you should pass it into the check process as an argument. Otherwise that part will also fail because check expects one argument.

[complexgenome]

@bentsherman Thank you. I'm struggling with nextflow.

How do I know what's DSL1 syntax and/or otherwise?

I'm terrible sorry as I'm unable to follow you. I've been trying to send argument to fastp but I fail repeatedly.

So the fqpairs_ch should be defined in your workflow block

What is the workflow block?

and then you should pass it into the check process as an argument

I have not been able to do so. Do I decalre fastp as fastp or fastp() in another script?

If I put fastq_ch in workflow block, I get java error

workflow {
	check().view()
fqpairs_ch=channel.fromFilePairs('/Users/sariys01/Downloads/tiny/normal/*_R{1,2}_xxx.fastq.gz')
	fastp(fqpairs_ch).view()
}

Error: attached.

[bentsherman]

I gave another look and I am seeing multiple errors, so I will just correct the code and show you what I changed:

• don't need parentheses after fastp process name
• reference file pairs as x0 and x1 instead of x[0] and x[1]
• remove println from process output, emit your output files here instead

process fastp {

    tag "$sample_id"

    input:
    tuple val(sample_id), file(x0), file(x1)

    output:
    val(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 ${x0} -I ${x1} \
        -o fastp_trimmed/joinedfiles.dat_${x0} -O fastp_trimmed/joinedfiles.dat_${x1}
    """
}

workflow {
    fqpairs_ch = channel.fromFilePairs('/Users/sariys01/Downloads/tiny/normal/*_R{1,2}_xxx.fastq.gz')
    fastp(fqpairs_ch).view()
}

Let's get this part working first, then it should be easy for you to move your process into a separate module. Try this snippet with the rest of your code and let me know if it works.

[complexgenome]

@bentsherman Thanks for editing and reviewing code. It works, however there's one concern - it doesn't make directory as indicated at the working directory level. It errors out due to mismatch FASTQ paired end reads; however, not creating directory is mysterious.

output_log.txt

ls ./*/*
ls work/22/697720257efeeacd51d21a4f84f2d0/fastp_trimmed

Next, how do I keep process in a separate file and send parameters?

Thank you again.

[bentsherman]

@sariya , I recommend that you refer to our training resources such as https://training.nextflow.io/ , so that you can acquire a proper understanding of how to use Nextflow. That will be much more effective than working through errors one at a time here.

[complexgenome]

@bentsherman Thank you for your time and replies.