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fix: Update to the latest version of nextclade. #1701

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merged 5 commits into from
Aug 16, 2024
Merged

fix: Update to the latest version of nextclade. #1701

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11d2b5b
Update to the latest version of nextclade.
jgadling Aug 16, 2024
224d3c0
Fix tests
jgadling Aug 16, 2024
d6912a5
Fix git error.
jgadling Aug 16, 2024
66a354c
update the db instead of the code.
jgadling Aug 16, 2024
db1a67c
Fix lint.
jgadling Aug 16, 2024
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2 changes: 1 addition & 1 deletion src/backend/Dockerfile.lineage_qc
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Expand Up @@ -19,7 +19,7 @@ RUN update-ca-certificates

# install nextclade, check it installed correctly
RUN apt-get --yes install curl
RUN cd /usr/local/bin && curl -fsSL "https://github.com/nextstrain/nextclade/releases/download/2.14.0/nextclade-x86_64-unknown-linux-gnu" -o "nextclade" && chmod +x nextclade
RUN cd /usr/local/bin && curl -fsSL "https://github.com/nextstrain/nextclade/releases/download/3.8.2/nextclade-x86_64-unknown-linux-gnu" -o "nextclade" && chmod +x nextclade
RUN nextclade --version

# Poetry: install app
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1 change: 1 addition & 0 deletions src/backend/aspen/workflows/nextclade/prep_samples.py
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Expand Up @@ -15,6 +15,7 @@
if you're tweaking it to support multiple tools. Especially look closely at
the function `get_sample_ids_to_refresh` in here.
"""

import io
import json
import subprocess
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2 changes: 1 addition & 1 deletion src/backend/aspen/workflows/nextclade/run_nextclade.sh
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Expand Up @@ -20,7 +20,7 @@ shopt -s inherit_errexit # no silent breaking
# This is where we will store Nextclade's dataset for the target pathogen.
NEXTCLADE_DATASET_DIR=nextclade_dataset_bundle
# Inside the dataset, Nextclade uses this file to tag the dataset.
NEXTCLADE_TAG_FILENAME=tag.json
NEXTCLADE_TAG_FILENAME=pathogen.json

# Certain bits of info need to be passed around during the workflow.
# Using JSON file as an easy way to pass them around to various processes.
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