Nextflow stdout:

N E X T F L O W  ~  version 25.04.2
Launching `/home/runner/work/fetchngs/fetchngs/.nf-test-e184567e4bb5df640df6a4032ca393df.nf` [ridiculous_montalcini] DSL2 - revision: c7982b80dd
Downloading plugin [email protected]
Downloading plugin [email protected]
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
[09/50ed43] Submitted process > CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
ERROR ~ Error executing process > 'CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)'

Caused by:
  Process `CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)` terminated with an error exit status (126)


Command executed [/home/runner/work/fetchngs/fetchngs/modules/nf-core/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh]:

  #!/usr/bin/env bash
  
  set -u
  
  
  # Get the expected NCBI settings path and define the environment variable
  # `NCBI_SETTINGS`.
  eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
  
  # If the user settings do not exist yet, create a file suitable for `prefetch`
  # and `fasterq-dump`. If an existing settings file does not contain the required
  # values, error out with a helpful message.
  if [[ ! -f "${NCBI_SETTINGS}" ]]; then
      printf '/LIBS/GUID = "5a7f0b97-ddac-4736-8547-86e55e410c95"\n/libs/cloud/report_instance_identity = "true"\n' > 'user-settings.mkfg'
  else
      prefetch --help &> /dev/null
      if [[ $? = 78 ]]; then
          echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
          "missing the required entries for /LIBS/GUID and"\
          "/libs/cloud/report_instance_identity."\
          "Feel free to add the following to your settings file:" >&2
          echo "$(printf '/LIBS/GUID = "5a7f0b97-ddac-4736-8547-86e55e410c95"\n/libs/cloud/report_instance_identity = "true"\n')" >&2
          exit 1
      fi
      fasterq-dump --help &> /dev/null
      if [[ $? = 78 ]]; then
          echo "You have an existing vdb-config at '${NCBI_SETTINGS}' but it is"\
          "missing the required entries for /LIBS/GUID and"\
          "/libs/cloud/report_instance_identity."\
          "Feel free to add the following to your settings file:" >&2
          echo "$(printf '/LIBS/GUID = "5a7f0b97-ddac-4736-8547-86e55e410c95"\n/libs/cloud/report_instance_identity = "true"\n')" >&2
          exit 1
      fi
      if [[ "${NCBI_SETTINGS}" != *.mkfg ]]; then
          echo "The detected settings '${NCBI_SETTINGS}' do not have the required"\
          "file extension '.mkfg'." >&2
          exit 1
      fi
      cp "${NCBI_SETTINGS}" ./
  fi

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/sra-tools:3.0.8--h9f5acd7_0' locally
  3.0.8--h9f5acd7_0: Pulling from biocontainers/sra-tools
  642efca944a0: Pulling fs layer
  bd9ddc54bea9: Pulling fs layer
  af92850953fd: Pulling fs layer
  bd9ddc54bea9: Verifying Checksum
  bd9ddc54bea9: Download complete
  642efca944a0: Verifying Checksum
  642efca944a0: Download complete
  642efca944a0: Pull complete
  bd9ddc54bea9: Pull complete
  af92850953fd: Verifying Checksum
  af92850953fd: Download complete
  af92850953fd: Pull complete
  Digest: sha256:6a6eb88399dba1faeb72cdec55369e7cec246889a62d4491d2c3a21d97b5de26
  Status: Downloaded newer image for quay.io/biocontainers/sra-tools:3.0.8--h9f5acd7_0
  /bin/bash: line 11: .command.run: Permission denied

Work dir:
  /home/runner/work/fetchngs/fetchngs/~/tests/e184567e4bb5df640df6a4032ca393df/work/09/50ed43936ff65d5b7d187120460069

Container:
  quay.io/biocontainers/sra-tools:3.0.8--h9f5acd7_0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/home/runner/work/fetchngs/fetchngs/~/tests/e184567e4bb5df640df6a4032ca393df/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr: