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Use ncov/ as a standalone directory #921

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Use ncov/ as a standalone directory #921

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4b6bdd2
prefix parameters.yaml defaults with ncov/
victorlin Apr 7, 2022
899f6c1
Revert "prefix parameters.yaml defaults with ncov/"
victorlin Apr 8, 2022
7828b5d
parameters.yaml: remove outgroup default
victorlin Apr 8, 2022
f4ffc85
use workflow.source_path on default files
victorlin Apr 12, 2022
4709e56
[wip] use workflow.source_path on scripts
victorlin Apr 12, 2022
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1 change: 0 additions & 1 deletion defaults/parameters.yaml
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Expand Up @@ -58,7 +58,6 @@ files:
reference: "defaults/reference_seq.gb"
alignment_reference: "defaults/reference_seq.fasta"
annotation: "defaults/annotation.gff"
outgroup: "defaults/outgroup.fasta" # is this arg still used? file doesn't exist in gh repo
ordering: "defaults/color_ordering.tsv"
color_schemes: "defaults/color_schemes.tsv"
auspice_config: "defaults/auspice_config.json"
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1 change: 1 addition & 0 deletions scripts/__init__.py
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@@ -0,0 +1 @@
# placeholder for relative imports
2 changes: 1 addition & 1 deletion scripts/sanitize_metadata.py
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Expand Up @@ -9,7 +9,7 @@
import sys
from tempfile import NamedTemporaryFile

from utils import extract_tar_file_contents
from .utils import extract_tar_file_contents

# Define all possible geographic scales we could expect in the GISAID location
# field.
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2 changes: 1 addition & 1 deletion scripts/sanitize_sequences.py
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Expand Up @@ -5,7 +5,7 @@
import re
import sys

from utils import stream_tar_file_contents
from .utils import stream_tar_file_contents


class DuplicateSequenceError(ValueError):
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