Bug report of germline post-calling qc module

[colenr]

In GitLab by wenluo Sep 17, 2021, 18:53

Error message during no report pipeline execution with only post calling QC:

. /etc/profile.d/modules.sh; module load python/2.7.5 glu;sh ./modules/post_calling_table.sh postcalling_qc/variants_annotated_basechange.txt postcalling_qc;glu util.join -1 SAMPLE -2 ANALYSISID -j inner postcalling_qc/titv.txt coverage/Final_merged_coverage.txt -o postcalling_qc/titv_tmp.txt:c=SAMPLE,TOTAL,TI,TV,RATIO,CACO,COV; mv postcalling_qc/titv_tmp.txt postcalling_qc/titv.txt GLU (unknown) module: util.join Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.

[Errno 2] No such file or directory: 'coverage/Final_merged_coverage.txt'

[Fri Sep 17 01:50:36 2021] Execution aborted due to input/output error [Fri Sep 17 01:50:36 2021] Error in rule postcalling_qc_table: jobid: 0 output: postcalling_qc/titv.txt, postcalling_qc/basechange_all.txt

Cause:

Snakefile_postcalling_qc requires coverage_dir + '/Final_merged_coverage.txt' at rule postcalling_qc_table. When coverage_check is set FALSE in config.yaml but post_calling_check is set TRUE. postcalling_qc_table will fail to find necessary input.