From 1c54c0b1ae684dba97345a136b802b5ef8e31e4d Mon Sep 17 00:00:00 2001 From: Mahesh Binzer-Panchal Date: Tue, 3 May 2022 16:02:11 +0200 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Matthieu Muffato --- modules/busco/main.nf | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/modules/busco/main.nf b/modules/busco/main.nf index 4ba4baac..c011b05b 100644 --- a/modules/busco/main.nf +++ b/modules/busco/main.nf @@ -24,20 +24,14 @@ process BUSCO { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}-${lineage}" def busco_config = config_file ? "--config $config_file" : '' - def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : '' + def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : '' """ # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute) # Check for container variable initialisation script and source it. if [ -f "/usr/local/env-activate.sh" ]; then - # . "/usr/local/env-activate.sh" # Errors out because of various unbound variables - export PATH='/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin' - export CONDA_PREFIX='/usr/local' - export CONDA_SHLVL='1' - export CONDA_DEFAULT_ENV='/usr/local' - export CONDA_PROMPT_MODIFIER='' - . "/usr/local/etc/conda/activate.d/activate-r-base.sh" - . "/usr/local/etc/conda/activate.d/augustus.sh" - . "/usr/local/etc/conda/activate.d/openjdk_activate.sh" + set +u # Otherwise, errors out because of various unbound variables + . "/usr/local/env-activate.sh" + set -u fi # If the augustus config directory is not writable, then copy to writeable area