bioinformatics - Nextflow pipeline: Accessing files from a channel when handling single and multiple inputs - Stack Overflow

admin管理员组

文章数量:1122832

Question:

I'm setting up a Nextflow pipeline that can process both single and multiple sets of input files. When processing a single set of files, I want to use command-line arguments like:

nextflow run main.nf --fasta sample.fasta --hmmdb database.hmm

For multiple sets of files, I prefer to provide them via a CSV file:

nextflow run main.nf --input samples.csv

The samples.csv file looks like this:

fasta,hmmdb
sample1.fasta,database1.hmm
sample2.fasta,database2.hmm

Current Workflow:

Here's the relevant part of my main.nf script:

workflow {

    main:

    if (params.input != null) {
        // Read input CSV file
        input_ch = Channel
            .fromPath(params.input)
            .splitCsv(header: true)
            .map { row -> tuple(
                    file(row.fasta),
                    file(row.hmmdb)
                )
            }
        input_ch.view()
    } else {
        // Use conventional arguments
        input_ch = Channel.of(
            tuple(
                file(params.fasta),
                file(params.hmmdb)
            )
        )
    }
    ch_versions = Channel.empty()

    // Launch the main pipeline workflow
    ACTUAL_PIPELINE(
        input_ch,
        ch_versions
    )
    ch_versions = ch_versions.mix(ACTUAL_PIPELINE.out.versions)

    //...
}

And the ACTUAL_PIPELINE workflow:

workflow ACTUAL_PIPELINE {

    take:
    ch_params     // Channel containing tuples of [fasta_file, hmmdb_file]
    ch_versions   // Channel for version information

    main:

    // Attempting to access the files from the channel
    collected = ch_params.collect()
    fasta = collected[0]
    hmmdb = collected[1]

    // Rest of the pipeline
    //...

}

Problem:

When I try to collect the contents of ch_params using collect(), and then access the files with collected[0] and collected[1], I encounter the following error:

ERROR ~ Unexpected error [StackOverflowError]

1. How can I properly access or iterate over the files from ch_params within the ACTUAL_PIPELINE workflow?
2. Is there a Nextflow-specific way to handle both single and multiple inputs efficiently without running into errors?

Thank you for your assistance!

Question:

I'm setting up a Nextflow pipeline that can process both single and multiple sets of input files. When processing a single set of files, I want to use command-line arguments like:

nextflow run main.nf --fasta sample.fasta --hmmdb database.hmm

For multiple sets of files, I prefer to provide them via a CSV file:

nextflow run main.nf --input samples.csv

The samples.csv file looks like this:

fasta,hmmdb
sample1.fasta,database1.hmm
sample2.fasta,database2.hmm

Current Workflow:

Here's the relevant part of my main.nf script:

workflow {

    main:

    if (params.input != null) {
        // Read input CSV file
        input_ch = Channel
            .fromPath(params.input)
            .splitCsv(header: true)
            .map { row -> tuple(
                    file(row.fasta),
                    file(row.hmmdb)
                )
            }
        input_ch.view()
    } else {
        // Use conventional arguments
        input_ch = Channel.of(
            tuple(
                file(params.fasta),
                file(params.hmmdb)
            )
        )
    }
    ch_versions = Channel.empty()

    // Launch the main pipeline workflow
    ACTUAL_PIPELINE(
        input_ch,
        ch_versions
    )
    ch_versions = ch_versions.mix(ACTUAL_PIPELINE.out.versions)

    //...
}

And the ACTUAL_PIPELINE workflow:

workflow ACTUAL_PIPELINE {

    take:
    ch_params     // Channel containing tuples of [fasta_file, hmmdb_file]
    ch_versions   // Channel for version information

    main:

    // Attempting to access the files from the channel
    collected = ch_params.collect()
    fasta = collected[0]
    hmmdb = collected[1]

    // Rest of the pipeline
    //...

}

Problem:

When I try to collect the contents of ch_params using collect(), and then access the files with collected[0] and collected[1], I encounter the following error:

ERROR ~ Unexpected error [StackOverflowError]

1. How can I properly access or iterate over the files from ch_params within the ACTUAL_PIPELINE workflow?
2. Is there a Nextflow-specific way to handle both single and multiple inputs efficiently without running into errors?

Thank you for your assistance!

• bioinformatics
• nextflow

Share Improve this question Follow asked Nov 21, 2024 at 22:14 jllPonsjllPons 4311 silver badge66 bronze badges

Add a comment  | 

1 Answer 1

Sorted by: Reset to default 1

How can I properly access or iterate over the files from ch_params within the ACTUAL_PIPELINE workflow?

Note that ch_params is a channel, so calling the collect operator will also return a channel (specifically a value channel). It cannot be sliced like a List, which I think is the issue here. One solution might be to pass in a closure to transform each item before it is collected (assuming that is what is needed), for example:

workflow ACTUAL_PIPELINE {

   take:

   ch_params
   ch_versions

   main:

   fasta_ch = ch_params.collect { fasta, hmmdb -> fasta }
   hmmdb_ch = ch_params.collect { fasta, hmmdb -> hmmdb }

   ...
}

Is there a Nextflow-specific way to handle both single and multiple inputs efficiently without running into errors?

Consider instead using the nf-schema plugin. It supports sample sheet formats including CSV, TSV, JSON and YAML. You would still need to handle your single and multiple inputs somehow (an if/else statement like what you have already is fine), but it lets you at least validate your inputs thereby reducing errors. Specifically, it lets you validate your input parameters against a pipeline schema, as well as validate the contents of your sample sheet against a sample sheet schema. From the docs:

include { validateParameters; paramsSummaryLog; samplesheetToList } from 'plugin/nf-schema'

// Validate input parameters
validateParameters()

// Print summary of supplied parameters
log.info paramsSummaryLog(workflow)

// Create a new channel of metadata from a sample sheet passed to the pipeline through the --input parameter
ch_input = Channel.fromList(samplesheetToList(params.input, "assets/schema_input.json"))

There's really no way to avoid errors, but the Nextflow extension for VS Code should help with syntax highlighting etc:

https://github.com/nextflow-io/vscode-language-nextflow

本文标签：