Paired end file for STAR

[pbpayal]

Hello,
I am new to Nextflow. I am trying to create a script for test files to read paired end files for STAR and align. I have already created the index. But I keep getting error because the second file is not getting detected.

My files look like this -

ERR188044_chrX_1.fastq.gz ERR188245_chrX_1.fastq.gz ERR188337_chrX_1.fastq.gz ERR188428_chrX_1.fastq.gz
ERR188044_chrX_2.fastq.gz ERR188245_chrX_2.fastq.gz ERR188337_chrX_2.fastq.gz ERR188428_chrX_2.fastq.gz
ERR188104_chrX_1.fastq.gz ERR188257_chrX_1.fastq.gz ERR188383_chrX_1.fastq.gz ERR188454_chrX_1.fastq.gz
ERR188104_chrX_2.fastq.gz ERR188257_chrX_2.fastq.gz ERR188383_chrX_2.fastq.gz ERR188454_chrX_2.fastq.gz
ERR188234_chrX_1.fastq.gz ERR188273_chrX_1.fastq.gz ERR188401_chrX_1.fastq.gz ERR204916_chrX_1.fastq.gz
ERR188234_chrX_2.fastq.gz ERR188273_chrX_2.fastq.gz ERR188401_chrX_2.fastq.gz ERR204916_chrX_2.fastq.gz

#!/usr/bin/env nextflow

nextflow.enable.dsl=2

// Input parameters
params.reads	  = 'fastq/*_chrX_{1,2}.fastq.gz'  // Glob pattern for paired-end reads
params.genomeDir  = '/data/test_proj/INDEX/index'
params.gtf        = '/data/test_proj/ref/chrX.gtf'
params.outdir     = 'star_output'



// Check required parameters
if (!params.genomeDir || !params.gtf) {
    error "Missing required parameters: --genomeDir and/or --gtf"
}

// Process to run STAR
process STAR_ALIGN {
    tag "${sample_id}"

    publishDir "${params.outdir}", mode: 'copy'

    input:
	tuple val(sample_id), path(reads)
        path(genomeDir)
        path(gtf)

    output:
    path "${sample_id}_Aligned.sortedByCoord.out.bam"
    path "${sample_id}_ReadsPerGene.out.tab"

    script:
    """
      echo "Processing sample: ${sample_id}"
      echo "Reading files: ${reads[0} and ${reads[1]}"

    STAR \
	--runThreadN 16 \
        --runMode alignReads \
        --readFilesCommand zcat \
        --readFilesIn ${reads[0} ${reads[1]} \
        --genomeDir ${params.genomeDir} \
        --sjdbGTFfile ${params.gtf} \
        --twopassMode Basic \
        --outSAMtype BAM SortedByCoordinate \
        --outSAMunmapped Within \
        --quantMode GeneCounts \
        --outFileNamePrefix ${sample_id}_
    """
}

// Workflow 
workflow {
    // Load paired-end reads into a channel, automatically extracts sample IDs
    reads_ch = Channel.fromFilePairs(params.reads, flat: true)
    reads_ch.view()
    // Pass them to the process
    STAR_ALIGN(reads_ch,params.genomeDir,params.gtf)

My command -

nextflow run star.nf   --reads 'fastq/*_{1,2}.fastq.gz'   --genomeDir '/data/test_proj/INDEX/index'   --gtf '/data/test_proj/ref/chrX.gtf'

I get this ERROR:

Command exit status:
  102

Command output:
  Processing sample: ERR188044_chrX
  Reading files: ERR188044_chrX_1.fastq.gz and null

Command error:
  Processing sample: ERR188044_chrX
  Reading files: ERR188044_chrX_1.fastq.gz and null
  
  EXITING: because of fatal INPUT file error: could not open read file: null
  SOLUTION: check that this file exists and has read permision.
  
  May 19 10:37:25 ...... FATAL ERROR, exiting

What am I doing wrong?

Thanks,
Payal

[pbpayal]

I was able to fix it -

Error was caued due to the value - flat in the below code.
reads_ch = Channel.fromFilePairs(params.reads, flat: true)

It was working fine when I removed the flat option -
reads_ch = Channel.fromFilePairs(params.reads)