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Snakefile
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Snakefile
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import os
all_input = []
all_input.append(os.path.join(config["data_directory"], "args"))
if config.get("start_subsampling"):
all_input.append(config["subsampling"]["output_path"])
rule all:
input:
all_input
rule prepare_nextclade_dataset:
output:
nextclade_dataset = directory(os.path.join(config["data_directory"], "nextclade_sc2_dataset"))
params:
name = "sars-cov-2"
shell:
"""
nextclade dataset get --name {params.name} --output-dir {output.nextclade_dataset}
"""
rule run_nextclade:
input:
sequences = os.path.join(config["data_directory"], "rawdata/sequences.fasta"),
nextclade_dataset = os.path.join(config["data_directory"], "nextclade_sc2_dataset")
output:
nextclade_tsv = os.path.join(config["data_directory"], "nextclade.tsv")
params:
min_length = config["sequence_min_length"],
threads: 8
shell:
"""
nextclade run \
{input.sequences} \
--jobs {threads} \
--input-dataset {input.nextclade_dataset} \
--min-length {params.min_length} \
--output-tsv {output.nextclade_tsv} \
--quiet
"""
if config.get("covizu_tree"):
rule modify_covizu_tree:
input:
covizu_tree = os.path.join(config["data_directory"], "rawdata/timetree.nwk")
output:
modified_tree = os.path.join(config["data_directory"], "modified_tree.nwk")
shell:
"""
python3 scripts/modify_covizu_tree.py \
--covizu-tree {input.covizu_tree} \
--output {output.modified_tree}
"""
rule filter_sequences:
input:
metadata = os.path.join(config["data_directory"], "rawdata/metadata.tsv"),
nextclade_tsv = os.path.join(config["data_directory"], "nextclade.tsv"),
modified_tree = os.path.join(config["data_directory"], "modified_tree.nwk")
output:
strains = os.path.join(config["data_directory"], "strains.txt")
params:
genbank_accession = "--include-genbank-accession" if config.get("genbank_accession") else "",
shell:
"""
python3 scripts/filter_sequences.py \
--metadata {input.metadata} \
--nextclade-tsv {input.nextclade_tsv} \
--tree {input.modified_tree} \
{params.genbank_accession} \
--output {output.strains}
"""
else:
rule filter_sequences:
input:
metadata = os.path.join(config["data_directory"], "rawdata/metadata.tsv"),
nextclade_tsv = os.path.join(config["data_directory"], "nextclade.tsv")
output:
strains = os.path.join(config["data_directory"], "strains.txt")
params:
genbank_accession = "--include-genbank-accession" if config.get("genbank_accession") else "",
shell:
"""
python3 scripts/filter_sequences.py \
--metadata {input.metadata} \
--nextclade-tsv {input.nextclade_tsv} \
{params.genbank_accession} \
--output {output.strains}
"""
rule get_nonsynonymous:
input:
genome = "defaults/genome.csv",
strains = os.path.join(config["data_directory"], "strains.txt"),
nextclade_tsv = os.path.join(config["data_directory"], "nextclade.tsv"),
metadata = os.path.join(config["data_directory"], "rawdata/metadata.tsv")
output:
nonsynonymous = os.path.join(config["data_directory"], "nonsynonymous.txt")
shell:
"""
python3 scripts/get_nonsynonymous.py \
--genome {input.genome} \
--strains {input.strains} \
--nextclade-tsv {input.nextclade_tsv} \
--metadata {input.metadata} \
--output {output.nonsynonymous}
"""
rule get_key_sites:
input:
strains = os.path.join(config["data_directory"], "strains.txt"),
nonsynonymous = os.path.join(config["data_directory"], "nonsynonymous.txt"),
metadata = os.path.join(config["data_directory"], "rawdata/metadata.tsv")
output:
key_sites = os.path.join(config["data_directory"], "key_sites.txt")
shell:
"""
python3 scripts/get_key_sites.py \
--strains {input.strains} \
--nonsynonymous {input.nonsynonymous} \
--metadata {input.metadata} \
--output {output.key_sites}
"""
rule construct_haplotype_sequences:
input:
strains = os.path.join(config["data_directory"], "strains.txt"),
nextclade_tsv = os.path.join(config["data_directory"], "nextclade.tsv"),
key_sites = os.path.join(config["data_directory"], "key_sites.txt")
output:
haplotype_sequences = os.path.join(config["data_directory"], "haplotype_sequences.txt")
shell:
"""
python3 scripts/construct_haplotype_sequences.py \
--strains {input.strains} \
--nextclade-tsv {input.nextclade_tsv} \
--sites {input.key_sites} \
--output {output.haplotype_sequences}
"""
rule construct_divergent_pathways:
input:
haplotype_sequences = os.path.join(config["data_directory"], "haplotype_sequences.txt"),
metadata = os.path.join(config["data_directory"], "rawdata/metadata.tsv")
output:
divergent_pathways = os.path.join(config["data_directory"], "divergent_pathways.csv")
threads: 8
shell:
"""
python3 scripts/construct_divergent_pathways.py \
--threads {threads} \
--haplotypes {input.haplotype_sequences} \
--metadata {input.metadata} \
--output {output.divergent_pathways}
"""
rule get_infos:
input:
divergent_pathways = os.path.join(config["data_directory"], "divergent_pathways.csv"),
metadata = os.path.join(config["data_directory"], "rawdata/metadata.tsv"),
nextclade_tsv = os.path.join(config["data_directory"], "nextclade.tsv")
output:
infos = os.path.join(config["data_directory"], "infos.tsv")
params:
genbank_accession = "--include-genbank-accession" if config.get("genbank_accession") else ""
shell:
"""
python3 scripts/get_infos.py \
--divergent-pathways {input.divergent_pathways} \
--metadata {input.metadata} \
--nextclade-tsv {input.nextclade_tsv} \
{params.genbank_accession} \
--output {output.infos}
"""
rule get_arg_values:
input:
infos = os.path.join(config["data_directory"], "infos.tsv"),
reference_dir = "defaults/reference"
output:
args = directory(os.path.join(config["data_directory"], "args"))
shell:
"""
python3 scripts/get_arg_values.py \
--infos {input.infos} \
--reference-dir {input.reference_dir} \
--output {output.args}
"""
rule subsampling:
input:
infos = os.path.join(config["data_directory"], "infos.tsv"),
haplotype_sequences = os.path.join(config["data_directory"], "haplotype_sequences.txt"),
divergent_pathways = os.path.join(config["data_directory"], "divergent_pathways.csv")
output:
subsamples = config["subsampling"]["output_path"]
params:
description = "--description "+"\""+str(config["subsampling"]["description"])+"\"" if config["subsampling"].get("description") else "",
location = "\""+config["subsampling"]["location"]+"\"",
date_start = config["subsampling"]["date_start"],
date_end = config["subsampling"]["date_end"],
variants = "".join([" --variants "+"\""+v+"\"" for v in config["subsampling"]["variants"]]) if config["subsampling"].get("variants") else "",
size = config["subsampling"]["size"],
characteristic = config["subsampling"]["characteristic"],
seed = config["subsampling"]["seed"],
temporally_even = "--temporally-even" if config["subsampling"].get("temporally_even") else "",
genbank_accession = "--return-genbank-accession" if config.get("genbank_accession") else ""
shell:
"""
python3 scripts/ncov_sampling.py \
--infos {input.infos} \
--haplotypes {input.haplotype_sequences} \
--divergent-pathways {input.divergent_pathways} \
{params.description} \
--location {params.location} \
--date-start {params.date_start} \
--date-end {params.date_end} \
{params.variants} \
--size {params.size} \
--characteristic {params.characteristic} \
--seed {params.seed} \
{params.temporally_even} \
{params.genbank_accession} \
--output {output.subsamples}
"""