Skip to content

Use library_name for prefix #14

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.

Sign up for GitHub

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

Open
pontushojer wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Use library_name for prefix #14

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 2 additions & 5 deletions bulk_webincli.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -176,12 +176,9 @@ def row_processing(self, row):
"""
row = row.dropna() # Drop any fields with N/A in specified.
row_meta = row.to_dict() # Gets a row of metadata and keeps name of column as an index

prefix = row_meta.get("experiment_name").replace(" ", "_").replace("/", "_")

if (self.context == "reads"): # If reads are being submitted, get the name of the file to obtain a prefix
prefix_field = row_meta.get("uploaded file 1")
elif (self.context == "genome"): # If an un-annotated genome is being submitted get the name of the fasta file to obtain a prefix
prefix_field = row_meta.get("fasta")
prefix = Path(prefix_field).stem # Get just the name of the run without the file extensions (indexing 0 required as both are tuples)
manifest_file = Path(self.manifest_dir) / "Manifest_{}.txt".format(prefix)
return manifest_file

Expand Down