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workflow: give input data files unique names #85

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workflow: give input data files unique names #85

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12 changes: 6 additions & 6 deletions workflow/snakemake_rules/core.smk
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
'''
This part of the workflow expects input files

sequences = "data/sequences.fasta",
metadata = "data/metadata.tsv",
sequences = "data/{build_name}_sequences.fasta",
metadata = "data/{build_name}_metadata.tsv",

and will produce output files as

Expand All @@ -14,9 +14,9 @@ In addition, `build_dir` and `auspice_dir` need to be defined upstream.

rule wrangle_metadata:
input:
metadata = "data/metadata.tsv"
metadata = "data/{build_name}_metadata.tsv"
output:
metadata = "results/metadata.tsv"
metadata = "results/{build_name}_metadata.tsv"
params:
strain_id = lambda w: config.get('strain_id_field', 'strain')
shell:
Expand All @@ -36,8 +36,8 @@ rule filter:
- minimum genome length of {params.min_length}
"""
input:
sequences = "data/sequences.fasta",
metadata = "results/metadata.tsv",
sequences = "data/{build_name}_sequences.fasta",
metadata = "results/{build_name}_metadata.tsv",
exclude = config["exclude"]
output:
sequences = build_dir + "/{build_name}/filtered.fasta",
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4 changes: 2 additions & 2 deletions workflow/snakemake_rules/download_via_lapis.smk
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
rule download_sequences_via_lapis:
output:
sequences = "data/sequences.fasta",
sequences = "data/{build_name}_sequences.fasta",
shell:
"""
curl https://mpox-lapis.genspectrum.org/v1/sample/fasta --output {output.sequences}
"""

rule download_metadata_via_lapis:
output:
metadata = "data/metadata.tsv"
metadata = "data/{build_name}_metadata.tsv"
shell:
"""
curl https://mpox-lapis.genspectrum.org/v1/sample/details?dataFormat=csv | \
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12 changes: 6 additions & 6 deletions workflow/snakemake_rules/prepare.smk
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
rule download:
message: "Downloading sequences and metadata from data.nextstrain.org"
output:
sequences = "data/sequences.fasta.xz",
metadata = "data/metadata.tsv.gz"
sequences = "data/{build_name}_sequences.fasta.xz",
metadata = "data/{build_name}_metadata.tsv.gz"
params:
sequences_url = "https://data.nextstrain.org/files/workflows/monkeypox/sequences.fasta.xz",
metadata_url = "https://data.nextstrain.org/files/workflows/monkeypox/metadata.tsv.gz"
Expand All @@ -15,11 +15,11 @@ rule download:
rule decompress:
message: "Decompressing sequences and metadata"
input:
sequences = "data/sequences.fasta.xz",
metadata = "data/metadata.tsv.gz"
sequences = "data/{build_name}_sequences.fasta.xz",
metadata = "data/{build_name}_metadata.tsv.gz"
output:
sequences = "data/sequences.fasta",
metadata = "data/metadata.tsv"
sequences = "data/{build_name}_sequences.fasta",
metadata = "data/{build_name}_metadata.tsv"
shell:
"""
gzip --decompress --keep {input.metadata}
Expand Down