aspera CONDA_PREFIX error

[mniederhuber]

Description of the bug

Testing the dev branch withe aspera as download_method and getting the following error with process NFCORE_FETCHNGS:SRA:ASPERA_CLI

 .command.sh: line 3: CONDA_PREFIX: unbound variable

This may be associated with #274.

Command used and terminal output

#! /bin/bash
#SBATCH --mem=8G
#SBATCH -t 6:00:00
#SBATCH -p general
#SBATCH -o var/log/fetch-%j.out
#SBATCH -e var/log/fetch-%j.err

module load nextflow

nextflow -log var/log/.fetchngs run nf-core/fetchngs -r dev \
	-profile unc_longleaf \
	-params-file config/fetchngs_params.yaml

Relevant files

fetchngs_params.yaml:
input: 'sheets/srx_ids.csv'
download_method: 'aspera'
outdir: 'fetchngs-newData-devBranch-02'

System information

Nextflow 23.04.02
HPC
slurm
Singularity
RHEL8
fetchngs dev

[drpatelh]

This particular issue should be fixed in v1.12.0 that is due to be released today. You won't need to use any custom configuration. Please feel free to re-open if the issue persists.