Skip to content

Outgroup rooting the phylogenetic trees #59

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
j23414 wants to merge 7 commits into
base: main
Choose a base branch
from
Draft

Outgroup rooting the phylogenetic trees #59

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
9cc6180
Add Mopeia virus as an outgroup
j23414 Feb 28, 2025
1ec21d9
Phylogenetic: Use outgroup for rooting the tree
j23414 Feb 28, 2025
37bc3ed
Nextclade: Use outgroup for rooting the tree
j23414 Feb 28, 2025
91bff2e
Group reference files in segment folders
j23414 Feb 28, 2025
3be0145
Update pipelines with segment reference paths
j23414 Feb 28, 2025
3153b6b
fixup
j23414 Feb 28, 2025
9643d5b
Update dataset
j23414 Feb 28, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion ingest/defaults/config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ curate:
]

nextclade:
segment_reference: "../shared/lassa_{segment}.fasta"
segment_reference: "../phylogenetic/defaults/{segment}/reference.fasta"
min_seed_cover: 0.01
dataset: "../nextclade_data"
field_map:
Expand Down
2 changes: 1 addition & 1 deletion nextclade/defaults/config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ refine:
coalescent: "opt"
date_inference: "marginal"
clock_rate: 0.0006
root: "mid_point"
outgroup: "NC_006575"

ancestral:
inference: "joint"
Expand Down
2 changes: 1 addition & 1 deletion nextclade/rules/annotate_phylogeny.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ rule translate:
input:
tree = "results/tree.nwk",
node_data = "results/nt_muts.json",
reference = "../phylogenetic/defaults/lassa_gpc.gb"
reference = "../phylogenetic/defaults/gpc/reference.gb"
output:
node_data = "results/aa_muts.json"
log:
Expand Down
25 changes: 23 additions & 2 deletions nextclade/rules/construct_phylogeny.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,30 @@ This part of the workflow usually includes the following steps:
See Augur's usage docs for these commands for more details.
"""

rule add_outgroup:
"""Add outgroup"""
input:
alignment = "data/sequences.fasta",
outgroup = "../phylogenetic/defaults/gpc/outgroup.fasta",
output:
alignment_with_outgroup = "results/sequences_with_outgroup.fasta",
log:
"logs/add-outgroup.txt",
benchmark:
"benchmarks/add-outgroup.txt",
shell:
"""
augur align \
--sequences {input.outgroup} \
--existing-alignment {input.alignment} \
--output {output.alignment_with_outgroup} \
2>&1 | tee {log}
"""

rule tree:
"""Building tree"""
input:
alignment = "data/sequences.fasta"
alignment = "results/sequences_with_outgroup.fasta"
output:
tree = "results/tree_raw.nwk"
log:
Expand Down Expand Up @@ -64,7 +84,7 @@ rule refine:
coalescent = config['refine']['coalescent'],
date_inference = config['refine']['date_inference'],
clock_rate = config['refine']['clock_rate'],
root = lambda wildcards: config['refine']['root'],
root = lambda wildcards: config['refine']['outgroup'],
shell:
"""
augur refine \
Expand All @@ -80,5 +100,6 @@ rule refine:
--date-confidence \
--date-inference {params.date_inference} \
--root {params.root} \
--remove-outgroup \
2>&1 | tee {log}
"""
2 changes: 1 addition & 1 deletion nextclade_data/tree.json
View file
Open in desktop

Large diffs are not rendered by default.

8 changes: 4 additions & 4 deletions phylogenetic/defaults/config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,10 +33,10 @@ refine:
date_inference: "marginal"
literature_clock_rate: 0.00078 #Ehichioya et al. 2019
# Root the tree based on "mid_point" for treetime
root:
l: "mid_point"
s: "mid_point"
gpc: "mid_point"
outgroup:
l: "NC_006574"
s: "NC_006575"
gpc: "NC_006575"

ancestral:
inference: "joint"
Expand Down
2 changes: 2 additions & 0 deletions phylogenetic/defaults/gpc/outgroup.fasta
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
>NC_006575
atggggcagatagtcaccttctttcaagaggtgccacacatccttgaagaagtgatgaacattgtgctgatgaccctctcaatcttggccatcctaaagggcatctacaatgtgatgacctgtggaatcatcggtttgataacatttttgttcttgtgtgggagatcatgctcaagcatctataaggacaactatgagttcttctctttcgacctcgacatgtcttcactgaatgcaacgatgcctctctcctgctcaaagaacaactcccatcactacatccaagttgggaatgagacaggcctagagctgacattgacaaacactagcataattgatcataagttttgcaacctgtctgatgctcacaggaggaatctttatgacaaagcacttatgtcaatcttgacaacattccacctaagcattccagattttaaccaacatgaggcaatgtcatgtgattttaacggagggaagatctcagttcaatacaacctgtcccactcaaattatgtggatgccggcaaccactgtggcactattgcaaatggcattatggatgtttttagaagaatgtattggagcacctccctttcggttgcctctgacataagtgggactcaatgcatacagaccgattataagtatttgattattcagaacacatcatgggaggatcattgcatgttctcaagaccctcacccatgggatttttaagccttctgtcacagagaaccaggaatttctacatctcaagaagacttttgggtctttttacatggactttgagtgactcggaagggaacgacatgccaggtggttactgtctcacaaggtctatgctaatagggcttgatctgaaatgctttgggaacactgccattgcgaagtgtaatcaggcacatgatgaagaattctgtgacatgctccgcctttttgattttaataaacaagcaattagcaaactgaggtctgaagttcagcagagcataaatttgataaataaagctgtcaacgccctcatcaatgatcaactggtcatgaggaaccatttgagagatctaatgggtattccttattgcaactactctaagttttggtacttgaatgatactaggacagggagaacatccctcccaaagtgttggcttgtgaccaatgggtcatacctaaatgaaacccagttctcaacagaaattgagcaagaagccaataacatgttcactgacatgttgaggaaggagtatgagaaaaggcagagcacaacacctctggggttagtagatctttttgttttctccactagcttttatttgatctccgtgttcctccacctaatcaaaattccaacacatagacacataaaaggcaagccttgcccgaaaccacacagactcaatcacatggcaatctgttcctgtggcttctataagcaaccaggtctccccacacaatggaaaaggtga
0 shared/lassa_gpc.fasta → phylogenetic/defaults/gpc/reference.fasta
View file
Open in desktop
File renamed without changes.
0 phylogenetic/defaults/lassa_gpc.gb → phylogenetic/defaults/gpc/reference.gb
View file
Open in desktop
File renamed without changes.
2 changes: 2 additions & 0 deletions phylogenetic/defaults/l/outgroup.fasta
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
>NC_006574
atggggaaaacgcagtccaagggacagcccagcacaaatctcctcaaggagacagaaccaaggcatccagtaataccagatgccaggggaactggccctgaattctgcaagagctgctggttcgaaaggagggggttagtcaggtgcaacgatcactacctatgtttgaactgtcttacacttttacacacagtgtcagataggtgccccatctgcaaacacaaactacccttcagactagagctccagacccagccgacagcaccaccagaaatcccaccatcccaaaatcccccaccctacagcccctgaggcagaactccgccccgaagcccctcccaaacacccctcccctcccccccggggggaccccccgccggggctccccccggggggagatgcgcgagctgttctcggagcacctactcaatgtcgaggggaggccccacctcttcaaagaggggcctgcacagcctccctcttaatctaaacttcccctctgaagactggatcatcagtgaagcctgcgatctactgtagcagagactatagcctttaaaatctgcccagaagtcaattccggagaacactctagtaaggaagttttcgtagccttcaggcatgcatcgtcccacaacccctataatatcaagttgtagccagtgtagtccttggtccattctggatctcagcatcttgctcaaagatctctccaagatttcggaatgatcctccattagctcaccaataaaaacattaagatcctggtcatggatgttggggttgaagggcaggagtttcctggtcccttcaataaggtatcctgagtcaacaactaaggggatttcaacatgctcaggccctatatgcgtgaaatcatgttcctccaggtccaggatctcctcattcaataagacggacaagggtatcacatcaggaatgggggaactatccctcaagtagtcacaaatattttcagtggacagcaaccaaattgatgtggtttcccttttaaaccatgtagatgtctgtgcaactctccagcaatctttaattgcggatctttgaacactaccactgtaagttacatcaagggaatgaggcttgaataatccaccttccaacaccacccctttgaaaaggaggtggagactaaatttctctttcaatgattcaccctgacttctcacctgaaaatttactgtgacagaaatttgaacgctcccaacactgaggtcggcaaaagcttcaagcagctcacttaccgactcaaagacgtgctgctcggttaatcctgatgctatgagctgtcctaagtttagaattgctggtgcacattcaaagtccagccaagcataacctgagtaaagatcatgcctgtacatgggtctttcaacacccttataaataaccttttctataaaagaagaaaaggggccgaggttgtcaagcccttccgactcaggaattgaagatctatgtggaaaccaagtaaaagaacctaaagtcctgcttgttgcaacgaatggtctgatgaaggactcaaagtagatttgtctcaggaaattttgtaccacatcataagtggtcaccaccctttcatccgtgattgggagatgagacctctcatgtgctattgctaaatctgaagacagaaccacataatgctcttctctcttccacttgacaacatgagaaattaatgacattgcctcacaattcacatctagaaccacacaaagatcaagaaacttaatccttggtgtccacctcattttcgttgatgctaggtcactcatgaagggcaagaggtgtctctcaaatagagatgggtaaagtcttctgaatgagtgaataatatggttaaaccccaccttgtcttccaagagttttgtggtagtgggcttcattgggaaatagtcacatggcttgaagggaattgaggatgttttctccttcactttgggttcacccaacacccaggaacccagctcaagtgatgtagataaggctatgcagaagtaatcccaaaggacaggtctcaagaaacctaacgcttcctcagctgcctttgtgtgctccttacccaagatccaaagatcgacgcccttaactttcaagctggaaacagaatccaatgctgacagtcttgaaactaatgattttatataggcggtggacctatctgagaatcgaacacatttgctacctagtgtcttgcaaagacctatgaaacctgatgctatcccactctgaaaggcacttttgttgacggcttcacagagcaacttttgtgcccctcttgtgaaattagaggataacttgctttgcaatgttttcaccaaggtaggcagtttttcttccccgagttcaacagcacctgtgtaaatgaccttctgtctcatgaccatctttaaagggtgatgagttgtcaaattaagccaacacaccgataaatcctcttctgagagggtgtcatcaccaacaaggctggtaagtttcttgaaggaatctgcggggtctcctgacaagtagatggctgtgaattcttcatgaagctctcctaatttcagcttattaaaaactgtccttaggaccttcctaactttctgagtgctttctggtaggattgcctcaatgttcctcataatcctatagcccctattgccatcaacccaatctttaacatcagaatccaaaaacaacaagaaaggatcaatgggatattgtgcatatctaagtagattcagtgttctctcctgaatagcgttacatagtgtgacaggcacaccattggccactgactgatcaatgatagtgtcaatagtttcagctaattgatgtggctccttacacttaacgttgtggagggcggcagccacgaatttcgttaacaatggaacttcatcaccccagacataaaaccttgatttgaactcagcaacaaatgaaccaataacactctttggactgatgaatttattcaattgatcacttaggaaatagtgaaattctagaatggcttggaattcctcaggctcatttgagagtaaatctgaaagatccttgccaaatagtgatatttgatcatcactagaggtatatgaatcaacttcatcttcaaatagacacttaatgcaataatttatgaatctctcactcactagaccgtagaagtcagaagcattgtgcaagatcccttgccccatgtcaattattgagctgagatgtgatggtattctgttttgtttaaagtattcaaagaagaaagcttctgttgacgtttggtggagtgattttttcaaacctaacctagacttaagataagatctcatcattgcattcacaacattgaaaggtacctcaattaacttgtgaatgtgccacgacagcaaagtggacacgtaatccttactttttatgtcctctatatcatctcttgtctcccatcgcaaattttgaagaaacaccaggaaaagaaaaggggacatcataggcccccacttgctgtgatcgaggctataagagacctgacctagtgaaacattcaatttcatggctagaatggcattgtggaattccttttcattattaagacagctccctctatattgcttagttagtgcctcaaaataatcctcaattaggcgtgtgaacatttttgtcctcaggtcacctatataaagttccctgttccctccaacttgttctttgtaagataaggaaaacttgagccttccagtatcaggacccaaggatgtgtatgactgtggggattcttgactgtaaaaacataggttctttagaactgcagttgtacaatttgtcaatgacagtgctttacctaatgcctcagaattgctctctctttcactgatcctaacatcattcatcagcctttctctatcaatcttgaagtttaggcatttgtttttgtaatggctgtattttccagccaatttccctgcattcatctgaagaagtagtgacttgaagcactgaaaaaactgctggtcattgaatgttctggtggagacagcttgggtgatgcatgttattgggcaagagtccaaggaatccaaatagaaatactttgatcttaactccaaatccttaaaaaagcctttgcagatcatctcataagcatctccaggtagtagtgactcatcaaaatcttccaccatgtggtgtgctatctctgcctggatcagtctgtagtaaacacagcccacatcttcagtacctaaaaccttcctcaagtctgtcaaggacttctcctctgacccatttcccacagggaacttcctgtcatatctatacttctcaaggacgacatcaacagatttcttcacatcctctagacagtcaagtgcacaactatccaagaataactcatctaattcgtcaggagccccttgtgaattgggatttgaggaacctgacttcttccccacaacaaggtcactaatggccttttgcaccttataatcataatcctccttactcaagaggtatttagttttcctctggaatacctctgatagctggcaaacagaagcagccactagtttatcatgatcgtaataaagtatcctctctccgtcagtatacttattcacaaccacacttttgttgcttgcaaggtcaagagctgttgcacacccagcagtaactaatggatctttaaacccacttaggtcatctcctttcttgaaaagagagccattgttaaaagaagacgtcatcattgagaagaattttcttgacacaccaggaactttataagatattctgttgttactcatactggtttctttggataaaaatttgtttgctgattcaagcagcagcatcctttcatcttcatccccctcttcagatgggttgatgttaatactgtcaaactccaacttgggctccaaatacttctcaaagcacttaatctgatctgtcaacctatctggagtttccttagttataaaatgacacatgtatgataggtttaacacaaacttaaatctattagtcaacatagtgctcaccccttcacccaggatgatgttgagaatgctcctcaccacactatacaagaggtgctccggctctgttatgagatcctccctcaacttttccattaactgcttatggtggaagtctgaaacaaaggccattatgaagtatcgcagaccttgcaagaacttctgtgctcttttgctagggttcacaagtatgaggatcatggtgattttgagcaataattttaaagttttttgttgatctctgagttctatacattcagacaaccaactcatcatggtgttgatagtctcatagataacacagtgtgagaaaattgcaggaaaaaacctttttggatctgcatagaatgaacaaatctcccccttctcaggattgttaatggcataacattttgagcactctcctgttttctgataaattaagttgaaattcccgcttcccatgataaagctttgattaaaagcttccttacaacgtacacgtttgtaccttgcagcaccatactcattttgcctcactttggctactgatgatgtcttcattgaattcaccaatgccaaagagatgctagatagtcttctcaggtcttctatggaatcagcttccaactcaataagagggtaggggaattgattcccctcttctttctcatagctcattgttggctgaatccctcttttctccattaacataagcctctcgtaactgtcctcctccagtatatcttcctctttaacataatctctaaagcacaaactggcagaggataatgcctctttggcctttgtgaggagtttgtttatgatgtcaaagaatataagctcagatctctgacacagagttcctacacctcccttcttcttcattgcactcaccattctcctttcaatccactttttaaggtccttttgtgtttcttgtagtgacaccaatctgtcgttcacacttaagaatgaggagccaagccattctgatcctaacagctcgccgtgacatttaagatcctttaagtgggccaaaaggatgattgcgtcaaaagtcagcattagttttcttctggtgttcaataactttagtgattttattttattcaacagtgacttccatccaggcacagagctttggaagtgattctgcaagcagctgtctcgatcaactccctcttgcctataacggtcgtagtcaccatagagcgctgttaccataggcgaggattttacaaacctctcttttagaggatcaatctctgagggtgtgtccccctctctgtcaatataaaggttgttgaaatctctcaagagctgtcgcctatctgtcctgacaaattgtctttctatctcaccctctttaagcttattcctaaaagcatgaaattctgatacaatctcttttttcacatcaagaatggacattttgttattgatgcctctgtggcagagctccaacaccctctcataatgatcagatcgagaatctgtcaaaacattgaggctctcaatgcccgatgttctcactcctgcttttgttaaagattcacaaagccttgagtactcagattcttcaaacatttttgatgactgctgcgagaattcaagtaagctaaataggatatgcctaaacctctcattggcccattctggaaacaaatcagtgtagaaattggttctgccgtctatcaagggcaacagaatgatgtcaacagatgataagtcaggctttaaagactctagcttaatggtatcttctttatacttttgctcaaagtttattggtgaagtcctgacaaagcattccagtaatattaatgtgttcccactgaatttgaatccatctggcaccacaaatggtagaccagggcacagaacaccttgtctctgcagaaggatttcaacagaaaggtcttctgagttgtgctcacaaccattggctttgcaactgtctatctcaatacagagtgacaacaacttaaggccctcaattaatagcattctcggctctgtctgaactaggaaggctagcttctgttttgaaagcctctcatcctctaagaggtacctgctcacaagatctttgctctcggacagcaactcctccat
0 shared/lassa_l.fasta → phylogenetic/defaults/l/reference.fasta
View file
Open in desktop
File renamed without changes.
0 phylogenetic/defaults/lassa_l.gb → phylogenetic/defaults/l/reference.gb
View file
Open in desktop
File renamed without changes.
2 changes: 2 additions & 0 deletions phylogenetic/defaults/s/outgroup.fasta
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
>NC_006575
atggggcagatagtcaccttctttcaagaggtgccacacatccttgaagaagtgatgaacattgtgctgatgaccctctcaatcttggccatcctaaagggcatctacaatgtgatgacctgtggaatcatcggtttgataacatttttgttcttgtgtgggagatcatgctcaagcatctataaggacaactatgagttcttctctttcgacctcgacatgtcttcactgaatgcaacgatgcctctctcctgctcaaagaacaactcccatcactacatccaagttgggaatgagacaggcctagagctgacattgacaaacactagcataattgatcataagttttgcaacctgtctgatgctcacaggaggaatctttatgacaaagcacttatgtcaatcttgacaacattccacctaagcattccagattttaaccaacatgaggcaatgtcatgtgattttaacggagggaagatctcagttcaatacaacctgtcccactcaaattatgtggatgccggcaaccactgtggcactattgcaaatggcattatggatgtttttagaagaatgtattggagcacctccctttcggttgcctctgacataagtgggactcaatgcatacagaccgattataagtatttgattattcagaacacatcatgggaggatcattgcatgttctcaagaccctcacccatgggatttttaagccttctgtcacagagaaccaggaatttctacatctcaagaagacttttgggtctttttacatggactttgagtgactcggaagggaacgacatgccaggtggttactgtctcacaaggtctatgctaatagggcttgatctgaaatgctttgggaacactgccattgcgaagtgtaatcaggcacatgatgaagaattctgtgacatgctccgcctttttgattttaataaacaagcaattagcaaactgaggtctgaagttcagcagagcataaatttgataaataaagctgtcaacgccctcatcaatgatcaactggtcatgaggaaccatttgagagatctaatgggtattccttattgcaactactctaagttttggtacttgaatgatactaggacagggagaacatccctcccaaagtgttggcttgtgaccaatgggtcatacctaaatgaaacccagttctcaacagaaattgagcaagaagccaataacatgttcactgacatgttgaggaaggagtatgagaaaaggcagagcacaacacctctggggttagtagatctttttgttttctccactagcttttatttgatctccgtgttcctccacctaatcaaaattccaacacatagacacataaaaggcaagccttgcccgaaaccacacagactcaatcacatggcaatctgttcctgtggcttctataagcaaccaggtctccccacacaatggaaaaggtgaagaacaggggcacccccgagacccaccgccttcggcggtgggtctcgggggcctggagtgactgttccttgatggcctccacgacccaccgccagaggcggtgggtcgtggaggtgtcccttcttacaggacaactctgggaggacctgttctaaacaccaggtctctactcaagactggtctgggggttggaatttgtggactccctatgactgctgcttcaaacatgagacaatccagcaatgcacagtgtggtgtcacttcttctttgccacctctcttcttcttttgcgttacaatccccgtatgcattctacaaaggtgtttgtattcatcccagatcttatcctcaaattttcttgcatcgtctttctgcatggacacatcaatcagttttatgtccctcctgttctgggagtcaagaagctttctgatgtcatcagcaccttgacacgacaagaccatgttctttggcaggctctcaattacagcacttgtcaaccccggctgaactgagaataggtcttggatgtcaatgccatgagagtgtttggagtcttgtttgaattgtttaatgtctgttggttccctgtaaaaatgaatatactgaccattattaggttgatagatagctatctccacggggtcttcaggtctcccttctatgtcaatccatgtcttagcatttggatccaattgcaacatgctgtctttgagttccattgtctgagagtaggtcaaaccagcaggcatgccttgggcctgagcgagtctgttggagttacctttgtcaggctttgcattctgttgcacatcaccactcagatcaacagttgtgttatcccaagccctgccgacgatcgatgttcttgatgctatgtaaggccaaccctctccagaaagacatagtttgtagaggagattttcataagggttcctttcccctggcgtgtcagagacaaacattcccaaagaacgcttgactttcaaggcagccttcaaaattccttccaaattggattttgttactttgatggtctccagcatgtttccgccgtctattagacaagcaccagctttcaccgcagctgacaggctaaaattgtaccctgatatgtttatggcacttttcttgggctcaatgatccccaagattgggtgggtctgagagagtttgtctaagtcagacatgtttggatactttgcagtgtacacaagccccaagtctgacaacgattggatcacatcattcagatctgcctgcccttgtttgcacatgcaagcaatcgtcaggcttggcattgtcccaaactgattgtttaaaagctctgggtttcgaacatcccacactctaacaatgccatctccgagagtgtttcctgcccggaacccgccacccattccgaccatctgtaacaaaaccctcctctgttctagctgctgagctgttaggttgcccatatagactccagcagcaagaggcctctcacctctgatgacttttgctttgagtctgtccaggtcggcagcaaggacgaggaggtcatcagaggttagtgtccccactctcaaaacattcttctgttggactgactttaactcaactagattgttcactgcctggtttaggtccctcaatcttttcaggtcagagtcatccctcttctcctttctcatcaacctttgaacattggcaacttcagagaagtccagcccatgaagaagtgcttgagcatccttgatgacttggatctttatgttggagcagtaccctgagagttctctcctcaggctctgtgtccacaagaaggacttcacctcctttgaattggacat
0 shared/lassa_s.fasta → phylogenetic/defaults/s/reference.fasta
View file
Open in desktop
File renamed without changes.
0 phylogenetic/defaults/lassa_s.gb → phylogenetic/defaults/s/reference.gb
View file
Open in desktop
File renamed without changes.
2 changes: 1 addition & 1 deletion phylogenetic/rules/annotate_phylogeny.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ rule translate:
input:
tree = "results/{segment}/tree.nwk",
node_data = "results/{segment}/nt_muts.json",
reference = "defaults/lassa_{segment}.gb"
reference = "defaults/{segment}/reference.gb"
output:
node_data = "results/{segment}/aa_muts.json"
log:
Expand Down
27 changes: 24 additions & 3 deletions phylogenetic/rules/construct_phylogeny.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,10 +19,30 @@ This part of the workflow usually includes the following steps:
See Augur's usage docs for these commands for more details.
"""

rule add_outgroup:
"""Add outgroup"""
input:
alignment = "results/{segment}/aligned.fasta",
outgroup = "defaults/{segment}/outgroup.fasta",
output:
alignment_with_outgroup = "results/{segment}/aligned_with_outgroup.fasta",
log:
"logs/{segment}/add-outgroup.txt",
benchmark:
"benchmarks/{segment}/add-outgroup.txt",
shell:
"""
augur align \
--sequences {input.outgroup} \
--existing-alignment {input.alignment} \
--output {output.alignment_with_outgroup} \
2>&1 | tee {log}
"""

rule tree:
"""Building tree"""
input:
alignment = "results/{segment}/aligned.fasta"
alignment = "results/{segment}/aligned_with_outgroup.fasta"
output:
tree = "results/{segment}/tree_raw.nwk"
log:
Expand Down Expand Up @@ -64,7 +84,7 @@ rule refine:
coalescent = config['refine']['coalescent'],
date_inference = config['refine']['date_inference'],
literature_clock_rate = config['refine']['literature_clock_rate'],
root = lambda wildcards: config['refine']['root'][wildcards.segment],
outgroup = lambda wildcards: config['refine']['outgroup'][wildcards.segment],
shell:
"""
augur refine \
Expand All @@ -78,7 +98,8 @@ rule refine:
--coalescent {params.coalescent} \
--date-confidence \
--date-inference {params.date_inference} \
--root {params.root} \
--root {params.outgroup} \
--remove-outgroup \
--clock-rate {params.literature_clock_rate} \
2>&1 | tee {log}
"""
2 changes: 1 addition & 1 deletion phylogenetic/rules/prepare_sequences.smk
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ rule align:
"""
input:
sequences = "results/{segment}/filtered.fasta",
reference = "defaults/lassa_{segment}.gb"
reference = "defaults/{segment}/reference.gb"
output:
alignment = "results/{segment}/aligned.fasta"
log:
Expand Down