Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Formatting of FASTQ paths in config is critical #30

Open
ijhoskins opened this issue May 7, 2024 · 0 comments
Open

Formatting of FASTQ paths in config is critical #30

ijhoskins opened this issue May 7, 2024 · 0 comments

Comments

@ijhoskins
Copy link

ijhoskins commented May 7, 2024

Not really an issue, just a quirk of setting up the config yaml file properly.

The following formatting does not work and leads to strange mappings in work/tmp/correspondence.txt and consequently an error similar to this (if do_check_file_existence : true):

ERROR ~ assert this_file.exists()
       |         |
       |         false
       /scratch/users/ihoskins/TEC/s

Incorrect formatting:

fastq:
AAVS1_KO_rep1: /scratch/users/ihoskins/TEC/TEC_1_R1.fq.gz

Correct formatting:

fastq:
AAVS1_KO_rep1:
- /scratch/users/ihoskins/TEC/TEC_1_R1.fq.gz

Conversely, the newline and hyphen is not required for specifying the reference files or metadata yaml files.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant