fastqc is not creating output (missing output files) which are expected by your output pattern.

Bugfixing

• check the fastqc work directory to see what files are being created
• try to set the output file expected to *.html

With nextflow you don't want to manage paths manually. Instead of creating a hardcoded path you should let it output the results into whatever directory it wants to, and catch them with an appropriate output declaration. Further processes should receive output by <process_name>.out or using the declared emit name. If you want to get the final results in a more convenient location the you should specify it using publishDir, preferentially using 'link' or 'symlink' modes (so you don't copy over large files).

Here's an example. I define FlyeTest process that will assemble CLR reads using flye. Flye's outputs the assembly into <dir>/assembly.fasta where you can specify <dir> with -o option, in my case it will be asm_out/assembly.fasta, and I tell nextflow to take this file as output. publishDir will create a hard link to FlyeTest output and place it in results directory.

A plain fromPath channel would create separate instances of FlyeTest() for each input file, with .collect() I can pass them as 1 array and .join(' ') them into a space separated string of paths.

I pass the value for read_path parameter as: 'data/Cell-?/seq-??.fastq.gz'. ? matches any digit, hence I can have up to 10 directories within data Cell-0 to Cell-9, each with up to 100 fastq files from seq-00 to seq-99.

    process FlyeTest {

    publishDir 'results', mode: 'link'

    input:
    path read_list

    output:
    path 'asm_out/assembly.fasta'

    script:
    """
    flye --pacbio-raw ${read_list.join(' ')} -o asm_out --threads ${task.cpus}
    ""
}

params.reads_path = './'
workflow {
    read_ch = channel.fromPath(params.reads_path)
        .collect()
        .view()
    FlyeTest(read_ch)
}


$ nextflow run FlyeTest.nf --reads_path 'data/Cell-?/seq-??.fastq.gz'

To make things cleaner I suggest setting params to generally acceptable default values (and if that's not possible adding checks) and writing a separate run.sh script with nextflow run <file_name>.nf --<param_name> <param_value> ...

This is a common issue that many learners encounter when working with Nextflow output management.

1. Use publishDir("${params.outdir}/...", mode: 'copy') to copy output files to a designated directory.
2. Use stdout instead of specifying individual output files(inlucding *)—this helps avoid missing any files that are generated dynamically or unexpectedly.

    process RNAseq_quality_check {
    publishDir ("${params.outdir}/01_quality_check", mode: 'copy') 
    input:          
        tuple val(sample_id), path(reads)
    output:
        stdout
    script:
    """
    mkdir -p ${params.outdir}/01_quality_check;
    fastqc ${reads[0]} ${reads[1]} -o ${params.outdir}/01_quality_check -t 8;
    """
    }