search

biosails / BioX-Workflow-Command

Other
0 stars 0 forks source link

Strange sample ".biosails" when running biox #30

Closed nizardrou closed 7 years ago

nizardrou commented 7 years ago

When running the following command, biox run -w fastqc.yml -o NCB-234-QC.sh in the following directory, /scratch/cz21/Chip_seq_Mouse/

The resulting workflow finds a sample called .biosails, and creates all data/processed relevant directories, [2017/09/18 11:10:25] Found samples: .biosails, Sample_Input, Sample_KOB-H2AZ, Sample_KOB-H3K27me3, Sample_KOB-H3K4me3, Sample_WTB-H2AZ, Sample_WTB-H3K27me3, Sample_WTB-H3K4me3

This is the sample rule in my YML conf, - file_rule: (Sample.*)$

This job will obviously fail, but only affecting the .biosails sample, still it seems that this shouldn't be matched according to the file rule.

jerowe commented 7 years ago

The new variable to declare the sample regexp is sample_rule, but it should be backwards compatible to file_rule, so this is still a bug.

I updated that workflow to use sample_rule, and it works as expected.