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Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
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Mahesh Binzer-Panchal 2022-05-03 16:02:11 +02:00 committed by GitHub
parent 6351ec745e
commit 1c54c0b1ae
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1 changed files with 4 additions and 10 deletions
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14
modules/busco/main.nf
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@ -24,20 +24,14 @@ process BUSCO {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}-${lineage}" def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
def busco_config = config_file ? "--config $config_file" : '' 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) # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
# Check for container variable initialisation script and source it. # Check for container variable initialisation script and source it.
if [ -f "/usr/local/env-activate.sh" ]; then if [ -f "/usr/local/env-activate.sh" ]; then
# . "/usr/local/env-activate.sh" # Errors out because of various unbound variables set +u # Otherwise, errors out because of various unbound variables
export PATH='/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin' . "/usr/local/env-activate.sh"
export CONDA_PREFIX='/usr/local' set -u
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"
fi fi
# If the augustus config directory is not writable, then copy to writeable area # If the augustus config directory is not writable, then copy to writeable area