我有一个Nextflow工作流,其中一个流程使用singularity.sif文件。
运行工作流后,我在日志中看到以下消息:
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMP as environment variable will not be supported in the future, use APPTAINERENV_TMP instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_TMPDIR as environment variable will not be supported in the future, use APPTAINERENV_TMPDIR instead
WARNING: DEPRECATED USAGE: Forwarding SINGULARITYENV_NXF_DEBUG as environment variable will not be supported in the future, use APPTAINERENV_NXF_DEBUG instead
我的nextflow.config如下所示
singularity {
enabled = true
autoMounts = true
}
conda {
conda = './env.yml'
enabled = true
}
//Wynton process Config
process {
executor = "sge"
scratch = true
stageInMode = "copy"
stageOUtMode="move"
errorStrategy = "retry"
clusterOptions = "-S /bin/bash -o job.log -e job.err"
withName: PROCESS_1 {
conda = './env.yml'
withName: SINGULARITY_PROGRAM {
container = 'program.sif'
}
...
}
1条答案
按热度按时间dddzy1tm1#
当项目移到Linux Foundation时,Singularity被重命名为Apptainer。所有的
$SINGULARITYENV_*
环境变量都已被弃用,并将在Apptainer的后续版本中删除。请注意,当Apptainer看到SINGULARITYENV环境变量时,它会警告您。我怀疑您收到这些警告是因为您的singularity
可能是apptainer
的符号链接,例如当安装版本1.1.3时就是这种情况。六天前,22.11.0-edge版本中添加了对Apptainer容器引擎的Nextflow支持。此边缘版本现在具有以下命令行选项:
要在Nextflow配置中启用它,请向Nextflow config添加以下内容(或将
singularity
块替换为):并使用最新版本运行您的工作流: