millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 02:58:17 +00:00
Code Issues Releases Packages Activity

Apply suggestions from code review

Browse source 
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
This commit is contained in:
Mahesh Binzer-Panchal 2022-05-03 16:02:11 +02:00 committed by GitHub
parent 6351ec745e
commit 1c54c0b1ae
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 4 additions and 10 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

14
modules/busco/main.nf
View file

@ -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