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Move uncompressed sequence and metadata files to the data folder
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Move uncompressed sequence and metadata files to the `data` folder
instead of the `results` folder. This change aligns with the monkeypox
and zika pipelines, smoothly allowing the example_data input files to be
in either compressed or uncompressed format during automated checks.
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j23414 committed Oct 11, 2023
1 parent 8ab810f commit 7e34cb6
Showing 1 changed file with 8 additions and 8 deletions.
16 changes: 8 additions & 8 deletions Snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -76,8 +76,8 @@ rule decompress:
sequences = "data/sequences_{serotype}.fasta.zst",
metadata = "data/metadata_{serotype}.tsv.zst"
output:
sequences = "results/sequences_{serotype}.fasta",
metadata = "results/metadata_{serotype}.tsv"
sequences = "data/sequences_{serotype}.fasta",
metadata = "data/metadata_{serotype}.tsv"
shell:
"""
zstd -d -c {input.sequences} > {output.sequences}
Expand All @@ -93,8 +93,8 @@ rule filter:
- excluding strains with missing region, country or date metadata
"""
input:
sequences = "results/sequences_{serotype}.fasta",
metadata = "results/metadata_{serotype}.tsv",
sequences = "data/sequences_{serotype}.fasta",
metadata = "data/metadata_{serotype}.tsv",
exclude = files.dropped_strains
output:
sequences = "results/filtered_{serotype}.fasta"
Expand Down Expand Up @@ -163,7 +163,7 @@ rule refine:
input:
tree = "results/tree-raw_{serotype}.nwk",
alignment = "results/aligned_{serotype}.fasta",
metadata = "results/metadata_{serotype}.tsv"
metadata = "data/metadata_{serotype}.tsv"
output:
tree = "results/tree_{serotype}.nwk",
node_data = "results/branch-lengths_{serotype}.json",
Expand Down Expand Up @@ -230,7 +230,7 @@ rule traits:
"""
input:
tree = "results/tree_{serotype}.nwk",
metadata = "results/metadata_{serotype}.tsv"
metadata = "data/metadata_{serotype}.tsv"
output:
node_data = "results/traits_{serotype}.json",
params:
Expand Down Expand Up @@ -271,7 +271,7 @@ rule export:
"""Exporting data files for for auspice"""
input:
tree = "results/tree_{serotype}.nwk",
metadata = "results/metadata_{serotype}.tsv",
metadata = "data/metadata_{serotype}.tsv",
branch_lengths = "results/branch-lengths_{serotype}.json",
traits = "results/traits_{serotype}.json",
clades = "results/clades_{serotype}.json",
Expand All @@ -298,7 +298,7 @@ rule export:
rule final_strain_name:
input:
auspice_json="results/raw_dengue_{serotype}.json",
metadata="results/metadata_{serotype}.tsv",
metadata="data/metadata_{serotype}.tsv",
root_sequence="results/raw_dengue_{serotype}_root-sequence.json",
output:
auspice_json="auspice/dengue_{serotype}.json",
Expand Down

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