From 39ece663024fe0b3a95ed1bbf8babf816400e0dc Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Fri, 8 Nov 2024 20:39:12 +0000 Subject: [PATCH 01/14] Add iqtree model extraction to augur_tree task and update workflow output --- .../augur/task_augur_tree.wdl | 15 +++++++++++++++ workflows/phylogenetics/wf_augur.wdl | 1 + 2 files changed, 16 insertions(+) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index f16c73618..a8b4f30ea 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -19,6 +19,9 @@ task augur_tree { # capture version information augur version > VERSION + # Get alignment basename + FASTA_BASENAME=$(basename ~{aligned_fasta} .fasta) + AUGUR_RECURSION_LIMIT=10000 augur tree \ --alignment "~{aligned_fasta}" \ --output "~{build_name}_~{method}.nwk" \ @@ -28,10 +31,22 @@ task augur_tree { ~{"--tree-builder-args " + tree_builder_args} \ ~{true="--override-default-args" false="" override_default_args} \ --nthreads auto + + # If iqtree, get the model used + if [ "~{method}" == "iqtree" ]; then + if [ "~{substitution_model}" == "auto" ]; then + MODEL=$(grep "Best-fit model:" ${FASTA_BASENAME}-delim.fasta.log | sed 's|Best-fit model: ||g;s|chosen.*||' | tr -d '\n\r') + else + MODEL="~{substitution_model}" + fi + echo "$MODEL" > 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 diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl index 3398d430f..e77c20fb5 100644 --- a/workflows/phylogenetics/wf_augur.wdl +++ b/workflows/phylogenetics/wf_augur.wdl @@ -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 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 From d181a1747fe503346f8d7463e1b78d828a08c162 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Fri, 8 Nov 2024 21:17:07 +0000 Subject: [PATCH 02/14] Refactor augur_tree task to correctly derive FASTA basename and directory for iqtree model extraction --- tasks/phylogenetic_inference/augur/task_augur_tree.wdl | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index a8b4f30ea..be6566595 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -19,9 +19,6 @@ task augur_tree { # capture version information augur version > VERSION - # Get alignment basename - FASTA_BASENAME=$(basename ~{aligned_fasta} .fasta) - AUGUR_RECURSION_LIMIT=10000 augur tree \ --alignment "~{aligned_fasta}" \ --output "~{build_name}_~{method}.nwk" \ @@ -35,7 +32,9 @@ task augur_tree { # If iqtree, get the model used if [ "~{method}" == "iqtree" ]; then if [ "~{substitution_model}" == "auto" ]; then - MODEL=$(grep "Best-fit model:" ${FASTA_BASENAME}-delim.fasta.log | sed 's|Best-fit model: ||g;s|chosen.*||' | tr -d '\n\r') + FASTA_BASENAME=$(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 From 2ac0c0d358ae92014d64e1d0224105e0da38f2a7 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Tue, 12 Nov 2024 14:42:38 +0000 Subject: [PATCH 03/14] Add iqtree model used field to augur workflow documentation --- docs/workflows/phylogenetic_construction/augur.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index 7ccf78d56..7e885d945 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -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 | | 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 | From a9a4e65a54a1880c6ca6992cdf966a4674f3d29a Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Tue, 12 Nov 2024 14:53:32 +0000 Subject: [PATCH 04/14] Handle empty substitution model case in augur_tree task --- tasks/phylogenetic_inference/augur/task_augur_tree.wdl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index be6566595..af50fb9f9 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -39,6 +39,8 @@ task augur_tree { MODEL="~{substitution_model}" fi echo "$MODEL" > FINAL_MODEL.txt + else + echo "" > FINAL_MODEL.txt fi >>> From 064d6778c01bf7f00ebf18a87a2cb6738fabdb07 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Tue, 12 Nov 2024 15:23:17 +0000 Subject: [PATCH 05/14] Ensure iqtree_model_used is a non-nullable String in augur_tree task and workflow --- tasks/phylogenetic_inference/augur/task_augur_tree.wdl | 2 +- workflows/phylogenetics/wf_augur.wdl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index af50fb9f9..22bd469e7 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -47,7 +47,7 @@ task augur_tree { output { File aligned_tree = "~{build_name}_~{method}.nwk" String augur_version = read_string("VERSION") - String? iqtree_model_used = read_string("FINAL_MODEL.txt") + String iqtree_model_used = read_string("FINAL_MODEL.txt") } runtime { docker: docker diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl index e77c20fb5..3a6b64ba9 100644 --- a/workflows/phylogenetics/wf_augur.wdl +++ b/workflows/phylogenetics/wf_augur.wdl @@ -203,7 +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 + String iqtree_model_used = augur_tree.iqtree_model_used 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 From 8e8f1f2a77a13bd13df6fa1835359ce8536573b1 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Thu, 14 Nov 2024 16:03:48 +0000 Subject: [PATCH 06/14] Update augur workflow documentation to include model options for substitution model and rename iqtree model variable for clarity --- docs/workflows/phylogenetic_construction/augur.md | 2 +- workflows/phylogenetics/wf_augur.wdl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index 7e885d945..24c53d8f7 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -220,7 +220,7 @@ This workflow runs on the set level. Please note that for every task, runtime pa | augur_tree | **exclude_sites** | File | File of one-based sites to exclude for raw tree building (BED format in .bed files, DRM format in tab-delimited files, or one position per line) | | Optional | | augur_tree | **method** | String | Which method to use to build the tree; options: "fasttree", "raxml", "iqtree" | iqtree | Optional | | augur_tree | **override_default_args** | Boolean | If true, override default tree builder arguments instead of augmenting them | FALSE | Optional | -| augur_tree | **substitution_model** | String | The substitution model to use; only available for iqtree. Specify "auto" to run ModelTest; options: "GTR" | GTR | Optional | +| augur_tree | **substitution_model** | String | The substitution model to use; only available for iqtree. Specify "auto" to run ModelTest; model options can be found [here](http://www.iqtree.org/doc/Substitution-Models) | GTR | Optional | | augur_tree | **tree_builder_args** | String | Additional tree builder arguments either augmenting or overriding the default arguments. FastTree defaults: "-nt -nosupport". RAxML defaults: "-f d -m GTRCAT -c 25 -p 235813". IQ-TREE defaults: "-ninit 2 -n 2 -me 0.05 -nt AUTO -redo" | | Optional | | sc2_defaults | **nextstrain_ncov_repo_commit** | String | The version of the from which to draw default values for SARS-CoV-2. | `23d1243127e8838a61b7e5c1a72bc419bf8c5a0d` | Optional | | organism_parameters | **gene_locations_bed_file** | File | Use to provide locations of interest where average coverage will be calculated | Defaults are organism-specific. Please find default values for some organisms here: . For an organism without set defaults, an empty file is provided, "gs://theiagen-public-files/terra/theiacov-files/empty.bed", but will not be as useful as an organism specific gene locations bed file. | Optional | diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl index 3a6b64ba9..bb003b705 100644 --- a/workflows/phylogenetics/wf_augur.wdl +++ b/workflows/phylogenetics/wf_augur.wdl @@ -203,7 +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 + String augur_iqtree_model_used = augur_tree.iqtree_model_used 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 From 548ca2696b04a90dd273bc944a6ff50c8d68ace5 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Thu, 14 Nov 2024 19:07:26 +0000 Subject: [PATCH 07/14] Add augur_iqtree_model_used variable to documentation for clarity --- docs/workflows/phylogenetic_construction/augur.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index 24c53d8f7..d8eb10f9f 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -284,13 +284,13 @@ The Nextstrain team hosts documentation surrounding the Augur workflow → Auspi | **Variable** | **Type** | **Description** | | --- | --- | --- | | aligned_fastas | File | A FASTA file of the aligned genomes | +| augur_iqtree_model_used | String | The iqtree model used during augur tree | | augur_phb_analysis_date | String | The date the analysis was run | | augur_phb_version | String | The version of the Public Health Bioinformatics (PHB) repository used | | augur_version | String | Version of Augur used | | 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 | | 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 | From a55fbbbe3cc3522d6a529b2b52299878953d3684 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Tue, 26 Nov 2024 20:37:20 +0000 Subject: [PATCH 08/14] added wildcard so we can parse the model name out of log file is a BED file is supplied by user for masking. also added DEBUG echo statement to see model string printed to log file. tested successfully w miniwdl both with and without BED file supplied and "auto" used as substitution_model input string --- tasks/phylogenetic_inference/augur/task_augur_tree.wdl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index 22bd469e7..da66ff47e 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -34,7 +34,7 @@ task augur_tree { 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') + 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 @@ -42,6 +42,9 @@ task augur_tree { else echo "" > FINAL_MODEL.txt fi + + echo + echo "DEBUG: FINAL_MODEL.txt is: $(cat FINAL_MODEL.txt)" >>> output { From d7737af9f387ea4b7b604fbbd7157f7829357147 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Mon, 2 Dec 2024 19:26:51 +0000 Subject: [PATCH 09/14] added "set --euo pipefail" to augur tree task, also added 2 output strings for mafft version and iqtree version. added these 2 output strings to Augur workflow --- .../phylogenetic_inference/augur/task_augur_tree.wdl | 12 ++++++++++++ workflows/phylogenetics/wf_augur.wdl | 2 ++ 2 files changed, 14 insertions(+) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index da66ff47e..d456ebef2 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -16,8 +16,18 @@ task augur_tree { String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0" } command <<< + set -euo pipefail + # capture version information augur version > VERSION + echo + echo "mafft version:" + mafft --version 2>&1 | tee MAFFT_VERSION + echo + echo "iqtree version:" + iqtree --version | grep version | sed 's/.*version/version/;s/ for Linux.*//' | tee IQTREE_VERSION + echo + echo "Running augur tree now..." AUGUR_RECURSION_LIMIT=10000 augur tree \ --alignment "~{aligned_fasta}" \ @@ -50,6 +60,8 @@ task augur_tree { output { File aligned_tree = "~{build_name}_~{method}.nwk" String augur_version = read_string("VERSION") + String mafft_version = read_string("MAFFT_VERSION") + String iqtree_version = read_string("IQTREE_VERSION") String iqtree_model_used = read_string("FINAL_MODEL.txt") } runtime { diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl index bb003b705..25b6c672c 100644 --- a/workflows/phylogenetics/wf_augur.wdl +++ b/workflows/phylogenetics/wf_augur.wdl @@ -204,6 +204,8 @@ workflow augur { File? time_tree = augur_refine.refined_tree File distance_tree = augur_tree.aligned_tree String augur_iqtree_model_used = augur_tree.iqtree_model_used + String augur_iqtree_version = augur_tree.iqtree_version + String augur_mafft_version = augur_tree.mafft_version 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 From 86be573b8cf49c1097e771be268619a461cd91ee Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Tue, 3 Dec 2024 21:57:45 +0000 Subject: [PATCH 10/14] added string output mafft_version to augur_align task; also added set -euo pipefail. tested successfully w miniwdl --- tasks/phylogenetic_inference/augur/task_augur_align.wdl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tasks/phylogenetic_inference/augur/task_augur_align.wdl b/tasks/phylogenetic_inference/augur/task_augur_align.wdl index 30065c8b2..e8cdca2a0 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_align.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_align.wdl @@ -12,8 +12,13 @@ task augur_align { String docker = "us-docker.pkg.dev/general-theiagen/biocontainers/augur:22.0.2--pyhdfd78af_0" } command <<< + set -euo pipefail + # capture version information augur version > VERSION + echo + echo "mafft version:" + mafft --version 2>&1 | tee MAFFT_VERSION # run augur align augur align \ @@ -26,6 +31,7 @@ task augur_align { output { File aligned_fasta = "alignment.fasta" String augur_version = read_string("VERSION") + String mafft_version = read_string("MAFFT_VERSION") } runtime { docker: docker From d8ccef56f10452e67bdaccf7c7a86958e305d2a2 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Wed, 4 Dec 2024 19:06:17 +0000 Subject: [PATCH 11/14] augur_tree task: added version capture for 3 tree building methods and thus 2 new String outputs. tested all 3 w miniwdl. Also updated augur wf to output these strings --- .../augur/task_augur_tree.wdl | 25 ++++++++++++++----- workflows/phylogenetics/wf_augur.wdl | 4 ++- 2 files changed, 22 insertions(+), 7 deletions(-) diff --git a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl index d456ebef2..a9a6b7b20 100644 --- a/tasks/phylogenetic_inference/augur/task_augur_tree.wdl +++ b/tasks/phylogenetic_inference/augur/task_augur_tree.wdl @@ -21,11 +21,23 @@ task augur_tree { # capture version information augur version > VERSION echo - echo "mafft version:" - mafft --version 2>&1 | tee MAFFT_VERSION - echo - echo "iqtree version:" - iqtree --version | grep version | sed 's/.*version/version/;s/ for Linux.*//' | tee IQTREE_VERSION + + # touch the version files to ensure they exist (so that read_string output function doesn't fail) + touch IQTREE_VERSION FASTTREE_VERSION RAXML_VERSION + + # capture version information only for the method selected by user OR default of iqtree + if [ "~{method}" == "iqtree" ]; then + echo "iqtree version:" + iqtree --version | grep version | sed 's/.*version/version/;s/ for Linux.*//' | tee IQTREE_VERSION + elif [ "~{method}" == "fasttree" ]; then + echo "fasttree version:" + # fasttree prints to STDERR, so we need to redirect it to STDOUT, then grep for line with version info, then cut to extract version number (and nothing else) + fasttree -help 2>&1 | grep -m 1 "FastTree" | cut -d ' ' -f 2 | tee FASTTREE_VERSION + elif [ "~{method}" == "raxml" ]; then + echo "raxml version:" + raxmlHPC -v | grep RAxML | sed -e 's/.*RAxML version //' -e 's/released.*//' | tee RAXML_VERSION + fi + echo echo "Running augur tree now..." @@ -60,8 +72,9 @@ task augur_tree { output { File aligned_tree = "~{build_name}_~{method}.nwk" String augur_version = read_string("VERSION") - String mafft_version = read_string("MAFFT_VERSION") String iqtree_version = read_string("IQTREE_VERSION") + String fasttree_version = read_string("FASTTREE_VERSION") + String raxml_version = read_string("RAXML_VERSION") String iqtree_model_used = read_string("FINAL_MODEL.txt") } runtime { diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl index 25b6c672c..7c76b02b1 100644 --- a/workflows/phylogenetics/wf_augur.wdl +++ b/workflows/phylogenetics/wf_augur.wdl @@ -200,12 +200,14 @@ workflow augur { String augur_version = augur_tree.augur_version # augur outputs + String? augur_mafft_version = augur_align.mafft_version File? auspice_input_json = augur_export.auspice_json File? time_tree = augur_refine.refined_tree File distance_tree = augur_tree.aligned_tree String augur_iqtree_model_used = augur_tree.iqtree_model_used String augur_iqtree_version = augur_tree.iqtree_version - String augur_mafft_version = augur_tree.mafft_version + String augur_fasttree_version = augur_tree.fasttree_version + String augur_raxml_version = augur_tree.raxml_version 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 From e476731a61d2dc1b4647ece3c370201d8d3a7532 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Tue, 10 Dec 2024 15:22:15 +0000 Subject: [PATCH 12/14] docs: add version variables for fasttree, iqtree, and raxml in augur workflow --- docs/workflows/phylogenetic_construction/augur.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index c9d144997..135ed7ea9 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -284,9 +284,12 @@ The Nextstrain team hosts documentation surrounding the Augur workflow → Auspi | **Variable** | **Type** | **Description** | | --- | --- | --- | | aligned_fastas | File | A FASTA file of the aligned genomes | +| augur_fasttree_version | String | The fasttree version used | | augur_iqtree_model_used | String | The iqtree model used during augur tree | +| augur_iqtree_version | String | The iqtree version used during augur tree | | augur_phb_analysis_date | String | The date the analysis was run | | augur_phb_version | String | The version of the Public Health Bioinformatics (PHB) repository used | +| augur_raxml_version | String | The version of raxml used during augur tree | | augur_version | String | Version of Augur used | | auspice_input_json | File | JSON file used as input to Auspice | | combined_assemblies | File | Concatenated FASTA file containing all samples | From 46068855183c43c6903ad057fb4f868e6064ceb7 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Tue, 10 Dec 2024 15:32:55 +0000 Subject: [PATCH 13/14] docs: add mafft version variable to augur workflow documentation --- docs/workflows/phylogenetic_construction/augur.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index 135ed7ea9..2375a6685 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -287,6 +287,7 @@ The Nextstrain team hosts documentation surrounding the Augur workflow → Auspi | augur_fasttree_version | String | The fasttree version used | | augur_iqtree_model_used | String | The iqtree model used during augur tree | | augur_iqtree_version | String | The iqtree version used during augur tree | +| augur_mafft_version | String | The mafft version used in augur align | | augur_phb_analysis_date | String | The date the analysis was run | | augur_phb_version | String | The version of the Public Health Bioinformatics (PHB) repository used | | augur_raxml_version | String | The version of raxml used during augur tree | From 34ead16e829417c39b752501c5035cadf421fec1 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Tue, 10 Dec 2024 15:39:34 +0000 Subject: [PATCH 14/14] docs: update descriptions for tree method version variables in augur workflow --- docs/workflows/phylogenetic_construction/augur.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index 2375a6685..88adb3c9f 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -284,13 +284,13 @@ The Nextstrain team hosts documentation surrounding the Augur workflow → Auspi | **Variable** | **Type** | **Description** | | --- | --- | --- | | aligned_fastas | File | A FASTA file of the aligned genomes | -| augur_fasttree_version | String | The fasttree version used | -| augur_iqtree_model_used | String | The iqtree model used during augur tree | -| augur_iqtree_version | String | The iqtree version used during augur tree | +| augur_fasttree_version | String | The fasttree version used, blank if other tree method used | +| augur_iqtree_model_used | String | The iqtree model used during augur tree, blank if iqtree not used | +| augur_iqtree_version | String | The iqtree version used during augur tree (defualt), blank if other tree method used | | augur_mafft_version | String | The mafft version used in augur align | | augur_phb_analysis_date | String | The date the analysis was run | | augur_phb_version | String | The version of the Public Health Bioinformatics (PHB) repository used | -| augur_raxml_version | String | The version of raxml used during augur tree | +| augur_raxml_version | String | The version of raxml used during augur tree, blank if other tree method used | | augur_version | String | Version of Augur used | | auspice_input_json | File | JSON file used as input to Auspice | | combined_assemblies | File | Concatenated FASTA file containing all samples |