Snakemake规则可以允许空的输出文件吗?

时间:2019-06-21 09:28:47

标签: python bioinformatics snakemake

我在snakemake工作流程中有一条规则,根据输入,该规则可能会产生一个空的输出文件。然后,在另一个规则中使用该输出文件,只要该输入文件存在路径,该命令的命令就完全可以使用空文件作为输入,并且仍然可以正确完成结果。有什么办法可以编写工作流程,使snakemake不会因为第一个规则产生了空文件而认为它失败了?

使用snakemake的一些输出进行编辑:

RuleException:
CalledProcessError in line 123 of /home/ckern/All_Species_Chromatin_Model/Snakefile:
Command ' set -euo pipefail;  grep E6$ Model_10/Cattle_Cortex_10_segments.bed > Model_10/Cattle_Cortex_10_E6.bed ' returned non-zero exit status 1.
  File "/home/ckern/All_Species_Chromatin_Model/Snakefile", line 123, in __rule_split_states
  File "/share/apps/conda3/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Removing output files of failed job split_states since they might be corrupted:
Model_10/Cattle_Cortex_10_E6.bed
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

0 个答案:

没有答案