fix conda env directive
@@ -164,7 +164,7 @@ rule subsample:
exclude_argument = lambda w: config["regions"][w.region][w.subsample].get("exclude", ""),
include_argument = lambda w: config["regions"][w.region][w.subsample].get("include", ""),
priority_argument = get_priority_argument
- conda: "../envs/nextstrain.yaml"
+ conda: config["conda_environment"]
shell:
"""
augur filter \
@@ -193,7 +193,7 @@ rule proximity_score:
priorities = REGION_PATH + "proximity_{focus}.tsv"
resources:
mem_mb = 4000
- conda: "../envs/nextstrain.yaml"
+ conda: config["conda_environment"]
shell:
"""
python3 scripts/priorities.py --alignment {input.alignment} \
@@ -212,7 +212,7 @@ rule subsample_regions:
lambda w: [REGION_PATH + f"sample-{subsample}.fasta" for subsample in config["regions"][w.region]]
output:
alignment = REGION_PATH + "subsampled_alignment.fasta"
- conda: "../envs/nextstrain.yaml"
+ conda: config["conda_environment"]
shell:
"""
python3 scripts/combine-and-dedup-fastas.py \
@@ -409,7 +409,7 @@ rule traits:
params:
columns = lambda w: config["traits"][w.region]["columns"],
sampling_bias_correction = lambda w: config["traits"][w.region]["sampling_bias_correction"]
- conda: "../envs/nextstrain.yaml"
+ conda: config["conda_environment"]
shell:
"""
augur traits \
@@ -542,7 +542,7 @@ rule export:
auspice_json = REGION_PATH + "ncov_with_accessions.json"
params:
title = export_title
- conda: "../envs/nextstrain.yaml"
+ conda: config["conda_environment"]
shell:
"""
augur export v2 \
