[Augur] Expose Augur versions

docs/workflows/phylogenetic_construction/augur.md

@@ -284,9 +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_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, 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 |

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

tasks/phylogenetic_inference/augur/task_augur_tree.wdl

@@ -16,8 +16,30 @@ 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
+
+    # 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..."
 
     AUGUR_RECURSION_LIMIT=10000 augur tree \
       --alignment "~{aligned_fasta}" \
@@ -34,19 +56,25 @@ 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
       echo "$MODEL" > FINAL_MODEL.txt
     else
       echo "" > FINAL_MODEL.txt
     fi
+
+    echo 
+    echo "DEBUG: FINAL_MODEL.txt is: $(cat FINAL_MODEL.txt)"
   >>>
 
   output {
     File aligned_tree  = "~{build_name}_~{method}.nwk"
     String augur_version = read_string("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 {

workflows/phylogenetics/wf_augur.wdl

@@ -200,10 +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_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