Hi! I am getting an error during `'NFCORE_CIRCRNACIRCRNACAT_FASTQ`:

ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:CAT_FASTQ (HC01)'

Caused by:
  Process `NFCORE_CIRCRNA:CIRCRNA:CAT_FASTQ (HC01)` terminated with an error exit status (126)


Command executed:

  cat input1/01-001_S1_L001_R1_001.fastq.gz > HC01_1.merged.fastq.gz
  cat input2/01-001_S1_L001_R2_001.fastq.gz > HC01_2.merged.fastq.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CIRCRNA:CIRCRNA:CAT_FASTQ":
      cat: $(echo $(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /scratch/azabala/network/circRNA/work_circRNA/aa/5a34573f047cf813261ee17db91ea1

Container:
  /home/azabala/.apptainer_cache/quay.io-nf-core-ubuntu-20.04.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Hey, would you mind open an issue on github? Makes it easier for me to keep track. This particular issue looks more related to your nextflow setup than with the #C01MKA377LM pipeline. So please include some information on your setup - e.g. which executor you are using. There is no logic in the pipeline that affects how this particular process is executed. Actually this particular process is a shared module across many pipelines and heavily tested in many different settings. Are you running a lot of nextflow/nf-core pipelines and have you encountered this before?

Hey Nico! I’ll open a GitHub issue so we can keep track of this. I’ve tested it with different samples and the problem persists; even scripts and setups that used to work no longer do. I’m currently running this on the dev branch. In other branches it seems to “work”, but some parameters are not up to date, so the behavior isn’t fully consistent. I’ll also try running it locally and on other machines to rule out any environment-specific issues.