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

Fix null path error for submission #192

Merged
merged 3 commits into from
Apr 4, 2024
Merged

Fix null path error for submission #192

merged 3 commits into from
Apr 4, 2024

Conversation

kyleoconnell
Copy link
Collaborator

Description

Modified the submission local modules to take val instead of path for unused parts of submission ch (tuple). For example, for sra submission, I changed fasta_path to val and then for genbank submission I changed the fastq inputs to val. These aren't used by the modules but this little hack avoids the null path error.

Checklist

Go Through Checklist Below and Place A ✔️ (X Inside the Box) if Completed

General Checks

  • Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

    For each relevant configuration:

    • Can the program run completely through without erroring out?
    • Does it produce the expected outputs, given the inputs provided?
  • Have you conducted proper linting procedures?

    • Numpy formatted docstrings for functions
    • Comments explaining lines of code
    • Consistent and intuitive naming conventions for variables, functions, classes, methods, attributes, and scripts
    • Single empty line between class functions, two lines between non-class functions, and two lines between imports and code body
    • Camel case formatting for class names
  • Have you updated existing documentation (README.md, etc.) or created new ones within docs?

CDC Checks

  • Did you check for sensitive data, and remove any?
  • If you added or modified HTML, did you check that it was 508 compliant?

Are additional approvals needed for this change? If so, please mention them below:

Are there potential vulnerabilities or licensing issues with any new dependencies introduced? If so, please mention them below:

@kyleoconnell kyleoconnell self-assigned this Apr 2, 2024
@kyleoconnell kyleoconnell changed the base branch from master to dev April 2, 2024 23:02
@jessicarowell jessicarowell merged commit 7495025 into dev Apr 4, 2024
@jessicarowell jessicarowell deleted the fix_null_path_kao branch April 4, 2024 19:28
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

Successfully merging this pull request may close these issues.

2 participants