Create channel of FASTQ file paths by parsing a CSV file

[James Ashmore]

I want to read a column from a text file which contains the paths to all of my FASTQ files. I then want to run each of these files through the various processes in my pipeline. I think I've successfully created the channel, but I am getting an error when I try and run the check process:

Script:

#!/usr/bin/env nextflow

designFile = file("design.tsv")
fastqChannel = Channel
                   .from(designFile)
                   .splitCsv(header: true)
                   .subscribe { row ->
                       println "${row.fastq}"
                   }

process check {
    input:
    file reads_fastq from fastqChannel

    output:
    file fastqc_html

    shell:
    """
    fastqc ${reads_fastq}
    """
}

Output:

$ ./main.nf check
N E X T F L O W  ~  version 0.19.1
Launching ./main.nf
A.fastq
B.fastq
C.fastq
[warm up] executor > local
ERROR ~ Channel `reads_fastq` has been used twice as an input by process `check` and another operator

 -- Check script 'main.nf' at line: 11 or see '.nextflow.log' file for more details

Any help greatly appreciated,
James

[Paolo Di Tommaso]

Hi, 

The problem in your example is that both the `subscribe` operator and the `check` process consume the same channel. 

To fix your example you can use the view operator in place of the subscribe. The main difference is that it implicitly creates a new channel that will be assigned to `fastqChannel`. For example: 

designFile = file("design.tsv")

fastqChannel = Channel

                   .from(designFile)

                   .splitCsv(header: true)

                   .view { row -> "${row.fastq}" }

process check {

    input:

    file reads_fastq from fastqChannel

    output:

    file fastqc_html

    shell:

    """

    fastqc ${reads_fastq}

    """

}

Hope it helps 

Paolo

--
You received this message because you are subscribed to the Google Groups "Nextflow" group.
To unsubscribe from this group and stop receiving emails from it, send an email to nextflow+u...@googlegroups.com.
Visit this group at https://groups.google.com/group/nextflow.
For more options, visit https://groups.google.com/d/optout.

[James Ashmore]

Works fine now, thank you