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[Augur] Add augur tree iqtree model type to output #674

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merged 7 commits into from
Nov 14, 2024
Merged

[Augur] Add augur tree iqtree model type to output #674

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39ece66
Add iqtree model extraction to augur_tree task and update workflow ou…
Michal-Babins Nov 8, 2024
d181a17
Refactor augur_tree task to correctly derive FASTA basename and direc…
Michal-Babins Nov 8, 2024
2ac0c0d
Add iqtree model used field to augur workflow documentation
Michal-Babins Nov 12, 2024
a9a4e65
Handle empty substitution model case in augur_tree task
Michal-Babins Nov 12, 2024
064d677
Ensure iqtree_model_used is a non-nullable String in augur_tree task …
Michal-Babins Nov 12, 2024
8e8f1f2
Update augur workflow documentation to include model options for subs…
Michal-Babins Nov 14, 2024
548ca26
Add augur_iqtree_model_used variable to documentation for clarity
Michal-Babins Nov 14, 2024
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1 change: 1 addition & 0 deletions docs/workflows/phylogenetic_construction/augur.md
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Expand Up @@ -290,6 +290,7 @@ The Nextstrain team hosts documentation surrounding the Augur workflow → Auspi
| auspice_input_json | File | JSON file used as input to Auspice |
| combined_assemblies | File | Concatenated FASTA file containing all samples |
| distance_tree | File | The distance tree created in Newick (.nwk) format |
| iqtree_model_used | String | The iqtree model used during augur tree |
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| keep_list | File | A list of samples included in the phylogenetic tree |
| metadata_merged | File | Tab-delimited text file of the merged augur_metadata input files from all samples |
| snp_matrix | File | The SNP distance matrix for all samples used in the phylogenetic tree |
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16 changes: 16 additions & 0 deletions tasks/phylogenetic_inference/augur/task_augur_tree.wdl
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Expand Up @@ -28,10 +28,26 @@ task augur_tree {
~{"--tree-builder-args " + tree_builder_args} \
~{true="--override-default-args" false="" override_default_args} \
--nthreads auto

# If iqtree, get the model used
if [ "~{method}" == "iqtree" ]; then
if [ "~{substitution_model}" == "auto" ]; then
FASTA_BASENAME=$(basename ~{aligned_fasta} .fasta)
FASTA_DIR=$(dirname ~{aligned_fasta})
MODEL=$(grep "Best-fit model:" ${FASTA_DIR}/${FASTA_BASENAME}-delim.iqtree.log | sed 's|Best-fit model: ||g;s|chosen.*||' | tr -d '\n\r')
else
MODEL="~{substitution_model}"
fi
echo "$MODEL" > FINAL_MODEL.txt
else
echo "" > FINAL_MODEL.txt
fi
>>>

output {
File aligned_tree = "~{build_name}_~{method}.nwk"
String augur_version = read_string("VERSION")
String iqtree_model_used = read_string("FINAL_MODEL.txt")
}
runtime {
docker: docker
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1 change: 1 addition & 0 deletions workflows/phylogenetics/wf_augur.wdl
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Expand Up @@ -203,6 +203,7 @@ workflow augur {
File? auspice_input_json = augur_export.auspice_json
File? time_tree = augur_refine.refined_tree
File distance_tree = augur_tree.aligned_tree
String iqtree_model_used = augur_tree.iqtree_model_used
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File aligned_fastas = select_first([augur_align.aligned_fasta, alignment_fasta])
File combined_assemblies = filter_sequences_by_length.filtered_fasta
File? metadata_merged = tsv_join.out_tsv
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