Test fail for AUGUSTUS _STAGECONFIG

SLURM SCRIPT

#!/bin/bash
#SBATCH --job-name=nf_genomeannotator_test
#SBATCH --output=nf_genomeannotator_test_%j.log
#SBATCH --error=nf_genomeannotator_test_%j.err
#SBATCH --time=24:00:00
#SBATCH --cpus-per-task=24
#SBATCH --mem=128G
##SBATCH --partition=batch

echo "Started"

module load nextflow
module load apptainer

mkdir -p ./apptainer_cache/{cache,tmp}
export NXF_SINGULARITY_CACHEDIR=./apptainer_cache/cache
export APPTAINER_CACHEDIR=./apptainer_cache/cache
export APPTAINER_TMPDIR=./apptainer_cache/tmp

nextflow run nf-core/genomeannotator -profile test,singularity --outdir ./test_results

echo "Complete"

ERROR

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_STAGECONFIG (config)'

Caused by:
Process NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_STAGECONFIG (config) terminated with an error exit status (1)

Command executed:

mkdir -p augustus_config
cp -R config/* augustus_config/

cat <<-END_VERSIONS > versions.yml
"NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_STAGECONFIG":
augustus: $(echo $(augustus | head -n1 | cut -f2 -d " " | sed "s/[)]//" | sed "s/[(]//" ))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
cp: can't stat 'config/*': No such file or directory

Work dir:
/gpfs1/home/a/b/abontemp/spider_fabian_nf_core_07182026/work/a7/6686d741f2ec827777326ed97f673b

Container:
/gpfs1/home/a/b/abontemp/spider_fabian_nf_core_07182026/./apptainer_cache/cache/depot.galaxyproject.org-singularity-augustus-3.4.0--pl5262h5a9fe7b_2.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

Start in the reported work directory and inspect the .command.sh file for NFCORE_GENOMEANNOTATOR:GENOMEANNOTATOR:AUGUSTUS_STAGECONFIG. Check why config/* is unavailable during the cp command, then rerun the provided SLURM test workflow. Done means the AUGUSTUS_STAGECONFIG process completes without the missing-config error.