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Snakefile
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Snakefile
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rule all:
input:
auspice = "auspice/results.json",
# Triggers the data and metadata preparation steps
rule prepare:
input:
"results/final_metadata.tsv",
"results/final_dataset.fasta",
"config/latlongs.tsv",
"config/colour_scheme.tsv"
# Define file names
rule files:
params:
contextual_sequences = "data/sequences.fasta",
new_sequences = "data/new_sequences.fasta",
aligned = "config/aligned.fasta",
metadata = "data/metadata.tsv",
new_metadata = "data/new_metadata.xlsx",
cache = "config/cache_coordinates.tsv",
lat_longs = "config/latlongs.tsv",
colscheme = "config/name2hue.tsv",
keep = "config/keep.txt",
ignore = "config/ignore.txt",
reference = "config/reference.gb",
clades = "config/clades.tsv",
auspice_config = "config/auspice_config.json",
# Define parameters
rule parameters:
params:
mask_5prime = 142,
mask_3prime = 548,
bootstrap = 1, # default = 1, but ideally it should be >= 100
model = "GTR",
root = "JF912185", # set one or more genomes to root the phylogeny
clock_rate = 0.0003,
clock_std_dev = 0.0001,
rule options:
params:
threads = 1
options = rules.options.params
files = rules.files.params
parameters = rules.parameters.params
rule add_sequences:
message:
"""
Filtering sequence files to:
- Add contextual and new sequences
- Prevent unwanted sequences from being incorporated in the initial dataset.
"""
input:
genomes = files.contextual_sequences,
new_sequences = files.new_sequences,
include = files.keep,
exclude = files.ignore
output:
sequences = temp("results/temp_dataset.fasta")
shell:
"""
python scripts/add_new_sequences.py \
--genomes {input.genomes} \
--new-genomes {input.new_sequences} \
--keep {input.include} \
--remove {input.exclude} \
--output {output.sequences}
"""
rule process_metadata:
message:
"""
Processing {input.genomes} and metadata files to:
- Include only metadata from sequences included in {input.genomes}
- Process metadata by dropping or adding columns, and fixing specific fields
"""
input:
genomes = rules.add_sequences.output.sequences,
metadata1 = files.metadata,
metadata2 = files.new_metadata
output:
final_metadata = "results/final_metadata.tsv",
final_sequences = "results/final_dataset.fasta",
rename = "results/trees/rename.tsv"
shell:
"""
python scripts/process_metadata.py \
--sequences {input.genomes} \
--metadata1 {input.metadata1} \
--metadata2 {input.metadata2} \
--time-var "date" \
--output1 {output.final_metadata} \
--output2 {output.final_sequences} \
--output3 {output.rename}
"""
rule coordinates:
message:
"""
Searching for coordinates (latitudes and longitudes) for samples in {input.metadata}
"""
input:
metadata = rules.process_metadata.output.final_metadata,
cache = files.cache
params:
columns = "country division location"
output:
latlongs = "config/latlongs.tsv"
shell:
"""
python scripts/get_coordinates.py \
--metadata {input.metadata} \
--columns {params.columns} \
--cache {input.cache} \
--output {output.latlongs}
cp {output.latlongs} config/cache_coordinates.tsv
"""
rule colours:
message:
"""
Assigning colour scheme for defined columns in {input.matrix}
"""
input:
matrix = rules.process_metadata.output.final_metadata,
scheme = files.colscheme,
params:
host = "host_type host",
geo = "region division location",
output:
colours1 = temp("config/col_hosts.tsv"),
colours2 = temp("config/col_geo.tsv"),
colour_scheme = "config/colour_scheme.tsv",
shell:
"""
python scripts/colour_maker.py \
--input {input.matrix} \
--colours {input.scheme} \
--levels {params.host} \
--output {output.colours1}
python scripts/colour_maker.py \
--input {input.matrix} \
--colours {input.scheme} \
--levels {params.geo} \
--output {output.colours2}
python scripts/multi_merger.py \
--path "./config" \
--regex "col_*" \
--columns "field, value, hex_color" \
--output {output.colour_scheme}
"""
### STARTING NEXTSTRAIN ANALYSES ###
### Aligning the sequences using MAFFT
rule align:
message:
"""
Aligning sequences to {input.reference}
- gaps relative to reference are considered real
"""
input:
sequences = rules.process_metadata.output.final_sequences,
aligned = files.aligned,
reference = files.reference,
params:
threads = options.threads
output:
alignment = "results/alignments/aligned.fasta"
shell:
"""
augur align \
--sequences {input.sequences} \
--reference-sequence {input.reference} \
--nthreads {params.threads} \
--output {output.alignment} \
--remove-reference
"""
# --existing-alignment {input.aligned} \
### Masking alignment sites
rule mask:
message:
"""
Mask bases in alignment
- masking {params.mask_from_beginning} from beginning
- masking {params.mask_from_end} from end
- masking other sites: {params.mask_sites}
"""
input:
alignment = rules.align.output.alignment
params:
mask_from_beginning = parameters.mask_5prime,
mask_from_end = parameters.mask_3prime,
mask_sites = "1" # set here any extra sites to be masked
output:
alignment = "results/alignments/masked.fasta"
shell:
"""
python scripts/mask-alignment.py \
--alignment {input.alignment} \
--mask-from-beginning {params.mask_from_beginning} \
--mask-from-end {params.mask_from_end} \
--mask-sites {params.mask_sites} \
--output {output.alignment}
"""
# ### Inferring tree with fewer bootstrap iterations
# rule tree:
# message: "Building tree"
# input:
# alignment = rules.mask.output.alignment
# params:
# threads = options.threads,
# output:
# tree = "results/trees/masked.tree"
# shell:
# """
# augur tree \
# --alignment {input.alignment} \
# --nthreads {params.threads} \
# --output {output.tree}
# """
rule tree:
message:
"""
"Building bootstrap tree"
"""
input:
alignment = rules.mask.output.alignment
params:
threads = options.threads,
bootstrap = parameters.bootstrap,
model = parameters.model,
output:
tree = "results/trees/masked.tree"
shell:
"""
iqtree \
-s {input.alignment} \
-b {params.bootstrap} \
-nt {params.threads} \
-m {params.model}
mv results/alignments/masked.fasta.treefile {output.tree}
"""
## Renaming taxa in bootstrap tree
rule rename:
message:
"""
Renaming taxa in bootstrap tree"
"""
input:
tree = rules.tree.output.tree,
names = rules.process_metadata.output.rename,
params:
format = "tree",
action = "rename"
output:
new_tree = "results/trees/final_tree.tree"
shell:
"""
python scripts/masterkey.py \
--input {input.tree} \
--format {params.format} \
--action {params.action} \
--list {input.names} \
--output {output.new_tree}
"""
### Running TreeTime to estimate time for ancestral genomes
rule refine:
message:
"""
Refining tree
- estimate timetree
- use {params.coalescent} coalescent timescale
- estimate {params.date_inference} node dates
"""
input:
tree = rules.rename.output.new_tree,
alignment = rules.mask.output.alignment,
metadata = rules.process_metadata.output.final_metadata
params:
root = parameters.root,
coalescent = "skyline",
clock_rate = parameters.clock_rate,
clock_std_dev = parameters.clock_std_dev,
date_inference = "marginal",
unit = "mutations"
output:
tree = "results/trees/tree.nwk",
node_data = "results/trees/branch_lengths.json"
shell:
"""
augur refine \
--tree {input.tree} \
--alignment {input.alignment} \
--metadata {input.metadata} \
--output-tree {output.tree} \
--output-node-data {output.node_data} \
--root {params.root} \
--timetree \
--coalescent {params.coalescent} \
--date-confidence \
--clock-filter-iqd 4 \
--clock-rate {params.clock_rate} \
--clock-std-dev {params.clock_std_dev} \
--divergence-units {params.unit} \
--date-inference {params.date_inference}
"""
### Reconstructing ancestral sequences and mutations
rule ancestral:
message:
"""
Reconstructing ancestral sequences and mutations"
"""
input:
tree = rules.refine.output.tree,
alignment = rules.mask.output.alignment
output:
node_data = "results/trees/nt_muts.json"
params:
inference = "joint"
shell:
"""
augur ancestral \
--tree {input.tree} \
--alignment {input.alignment} \
--inference {params.inference} \
--output-node-data {output.node_data}
"""
## Performing amino acid translation
rule translate:
message:
"""
Translating amino acid sequences"
"""
input:
tree = rules.refine.output.tree,
node_data = rules.ancestral.output.node_data,
reference = files.reference,
output:
node_data = "results/trees/aa_muts.json"
shell:
"""
augur translate \
--tree {input.tree} \
--ancestral-sequences {input.node_data} \
--reference-sequence {input.reference} \
--output {output.node_data} \
"""
### Inferring ancestral locations of genomes
rule traits:
message: "Inferring ancestral traits for {params.columns!s}"
input:
tree = rules.refine.output.tree,
metadata = rules.process_metadata.output.final_metadata,
params:
columns = "division location host_type"
output:
node_data = "results/trees/traits.json",
shell:
"""
augur traits \
--tree {input.tree} \
--metadata {input.metadata} \
--output {output.node_data} \
--columns {params.columns} \
--confidence
"""
### Define clades based on sets of mutations
rule clades:
message: " Labeling clades as specified in config/clades.tsv"
input:
tree = rules.refine.output.tree,
aa_muts = rules.translate.output.node_data,
nuc_muts = rules.ancestral.output.node_data,
clades = files.clades
output:
clade_data = "results/trees/clades.json"
shell:
"""
augur clades \
--tree {input.tree} \
--mutations {input.nuc_muts} {input.aa_muts} \
--clades {input.clades} \
--output {output.clade_data}
"""
### Generating final results for visualisation with auspice
rule export:
message: "Exporting data files for for auspice"
input:
tree = rules.refine.output.tree,
metadata = rules.process_metadata.output.final_metadata,
branch_lengths = rules.refine.output.node_data,
traits = rules.traits.output.node_data,
nt_muts = rules.ancestral.output.node_data,
aa_muts = rules.translate.output.node_data,
colors = rules.colours.output.colour_scheme,
lat_longs = rules.coordinates.output.latlongs,
clades = rules.clades.output.clade_data,
auspice_config = files.auspice_config,
output:
auspice = rules.all.input.auspice,
shell:
"""
augur export v2 \
--tree {input.tree} \
--metadata {input.metadata} \
--node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} {input.clades} \
--colors {input.colors} \
--lat-longs {input.lat_longs} \
--auspice-config {input.auspice_config} \
--output {output.auspice}
"""
### Clearing the working directory (only executed when needed)
rule clean:
message: "Removing directories: {params}"
params:
"config/colour_scheme.tsv",
"config/latlongs.tsv",
"config/aligned.fasta.ref.fasta",
"results",
"auspice"
shell:
"""
rm -rfv {params}
"""
rule reset:
message: "Removing directories: {params}"
params:
"results",
"auspice",
"data",
"config/colour_scheme.tsv",
"config/latlongs.tsv",
"results/sequence_dataset.fasta",
"data/rename.tsv"
shell:
"""
rm -rfv {params}
"""
rule delete:
message: "Deleting directory: {params}"
params:
"data",
"results"
shell:
"rm -rfv {params}"