Open lexie-lee opened 1 year ago
Hello @lexie-lee,
I apologize for taking a bit to respond to your issue I was in the midst of defending my thesis and wasn't checking the issue page regularly. I'm free now and can help you trouble shoot this.
Okay, the erroring step you showed is part of the new additions to the pipeline that incorporates gemBS as an alternative aligner to bwa-meth. But the step you showed is just one that is involved with setting up the config before the alignment starts this indicates that there are some issues with the pipeline finding your fastq files. Could you send me a screenshot of your /Volumes/PBLAB2/WGBS/Clean_Data dir I wanna make sure your file names will match the regular expression file gobbling in the config file. Also, remove the path indicated on the config to this sample csv file since you indicate all the sample information previously in the config. That is redundant and might be confusing the pipeline.
Here is the line I'm talking about. sample_fastq_csv: /Volumes/PBLAB2/WGBS/WGBSsample_group_high_ctrl.csv remove "/Volumes/PBLAB2/WGBS/WGBSsample_group_high_ctrl.csv"
Best, Jake
hello! thanks for building this tools! I met some problems when I try to deal with my WGBS data.
I tried to run wg-blimp from config file, but I went some error, it cannot be run successfully.
this is the log file:
this is my yaml file:
high ctrl.txt
Could you please help me on this? Thank you very much for your time.