search

databio / peppro

A modular, containerized pipeline for PRO-seq data processing
http://peppro.databio.org/
BSD 2-Clause "Simplified" License
10 stars 2 forks source link

UnboundLocalError: local variable 'trim_cmd1' referenced before assignment #39

Closed nsheff closed 5 years ago

nsheff commented 5 years ago

Looks like the read trimming command is named incorrectly:

Target exists: `/ext/yeti/processed/ppqc_test/results_pipeline/GSM3618128/fastq/GSM3618128_R1_processed.fastq`  
Traceback (most recent call last):
  File "/home/nsheff/code/peppro/pipelines/peppro.py", line 2896, in <module>
    sys.exit(main())
  File "/home/nsheff/code/peppro/pipelines/peppro.py", line 1529, in main
    outfolder=param.outfolder)
  File "/home/nsheff/code/peppro/pipelines/peppro.py", line 914, in _process_fastq
    "(", adapter_cmd, "|", trim_cmd1, ") 2> ", cutadapt_report])
UnboundLocalError: local variable 'trim_cmd1' referenced before assignment