Nextflow unzip gz file error: not a regular file

Question

I am new to Nextflow and I want to unzip a fastq.gz file. But It raised the error gunzip: SRR1659960_05pc_R1.fastq.gz is not a regular file. I tried to run the same command directly in my console, it works well. My Nextflow script is:

process gz_uncompress{
    input:
        path fastq_r1_gz_path
    output:
        path fastq_r1_path
    script:
    """
    gunzip -kd $fastq_r1_gz_path > "fastq_r1_path.fastq"
    """
}

workflow{
    gz_uncompress("/Users/test/PycharmProjects/nf-easyfuse/local_test/SRR1659960_05pc_R1.fastq.gz")
}

The error message is:

local_test ywan$ nextflow run t2.nf 
N E X T F L O W  ~  version 22.10.3
Launching `t2.nf` [peaceful_wilson] DSL2 - revision: bf9e3bc592
executor >  local (1)
[36/f8301b] process > gz_uncompress [  0%] 0 of 1
Error executing process > 'gz_uncompress'

Caused by:
  Process `gz_uncompress` terminated with an error exit status (1)

Command executed:

  gunzip -kd SRR1659960_05pc_R1.fastq.gz > "fastq_r1_path.fastq"

Command exit status:
  1
executor >  local (1)
[36/f8301b] process > gz_uncompress [100%] 1 of 1, failed: 1 ✘
Error executing process > 'gz_uncompress'

Caused by:
  Process `gz_uncompress` terminated with an error exit status (1)

Command executed:

  gunzip -kd SRR1659960_05pc_R1.fastq.gz > "fastq_r1_path.fastq"

Command exit status:
  1

Command output:
  (empty)

Command error:
  gunzip: SRR1659960_05pc_R1.fastq.gz is not a regular file

Work dir:
  /Users/test/PycharmProjects/nf-easyfuse/local_test/work/36/f8301b816e9eb834597ff1e6616c51

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

But when I ran gunzip -kd SRR1659960_05pc_R1.fastq.gz > "fastq_r1_path.fastq" in my console, there isn't any errors.

Could you please help me to figure out?

Answer 1

By default, Nextflow will try to stage process input files using symbolic links (this can be changed using the StageInMode directive). With gunzip, just make sure you write the output to stdout, using -c:

-c --stdout --to-stdout

Write output on standard output; keep original files unchanged. If there are several input files, the output consists of a sequence of independently compressed members. To obtain better compression, concatenate all input files before compressing them.

For example:

params.fastq = './test.fastq.gz'


process gunzip_fastq {

    input:
    path fastq_gz

    output:
    path fastq_gz.baseName

    script:
    """
    gunzip -c "${fastq_gz}" > "${fastq_gz.baseName}"
    """
}

workflow{

    fastq = file( params.fastq )

    gunzip_fastq( fastq )
}

On most systems, you could also just use zcat for this. The zcat command is identical to gunzip -c.