fix augur optional inputs (colors and genes) causing errors when runn…

…ing mpxv
theiagen · Oct 10, 2023 · 2a43d01 · 2a43d01
1 parent 785e8a0
commit 2a43d01
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Showing 2 changed files with 0 additions and 8 deletions.
diff --git a/tasks/utilities/task_augur_utilities.wdl b/tasks/utilities/task_augur_utilities.wdl
@@ -332,8 +332,6 @@ task set_mpxv_defaults { # establish mpxv default values for augur
     File mpxv_reference_fasta = "gs://theiagen-public-files-rp/terra/augur-mpox-references/reconstructed_ancestral_mpox.fasta"
     File mpxv_reference_genbank = "gs://theiagen-public-files-rp/terra/augur-mpox-references/NC_063383.1_reference.gb"
     File mpxv_auspice_config = "gs://theiagen-public-files-rp/terra/augur-mpox-references/mpox_auspice_config_mpxv.json"
-    File mpxv_gene_annotations_gff = "gs://theiagen-public-files-rp/terra/augur-mpox-references/genemap.gff"
-    File mpxv_colors = "gs://theiagen-public-files-rp/terra/augur-mpox-references/colors_mpxv.tsv"
 
     Int disk_size = 50
   }
@@ -349,8 +347,6 @@ task set_mpxv_defaults { # establish mpxv default values for augur
     File reference_fasta = mpxv_reference_fasta
     File reference_genbank = mpxv_reference_genbank
     File auspice_config = mpxv_auspice_config
-    File genes = mpxv_gene_annotations_gff
-    File colors = mpxv_colors
     # inherited from flu defaults
     Float min_date = 2020.0
     Int pivot_interval = 1

diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl
@@ -37,8 +37,6 @@ workflow augur {
     # these are very minimal files that hopefully will prevent workflow failure but will not provide any useful information
     File lat_longs_tsv = "gs://theiagen-public-files-rp/terra/augur-defaults/minimal-lat-longs.tsv"
     File auspice_config = "gs://theiagen-public-files-rp/terra/augur-defaults/minimal-auspice-config.json"
-    File genes = "gs://theiagen-public-files-rp/terra/augur-defaults/minimal-genes.tsv"
-    File colors = "gs://theiagen-public-files-rp/terra/augur-defaults/minimal-colors.tsv"
 
     Boolean distance_tree_only = false # by default, do not skip making a time tree
   }
@@ -112,7 +110,6 @@ workflow augur {
         refined_tree = augur_refine.refined_tree,
         ancestral_nt_muts_json = augur_ancestral.ancestral_nt_muts_json,
         reference_genbank = select_first([reference_genbank, sc2_defaults.reference_genbank, flu_defaults.reference_genbank, mpxv_defaults.reference_genbank]),
-        genes = select_first([mpxv_defaults.genes, genes]),
         build_name = build_name
     }
     if (flu_segment == "HA") { # we only have clade information for HA segments (but SC2 defaults will be selected first)
@@ -150,7 +147,6 @@ workflow augur {
                             augur_clades.clade_assignments_json,
                             augur_traits.traits_assignments_json]),
         build_name = build_name,
-        colors_tsv = select_first([mpxv_defaults.colors, colors]),
         lat_longs_tsv = select_first([sc2_defaults.lat_longs_tsv, flu_defaults.lat_longs_tsv, mpxv_defaults.lat_longs_tsv, lat_longs_tsv]),
         auspice_config = select_first([sc2_defaults.auspice_config, flu_defaults.auspice_config, mpxv_defaults.auspice_config, auspice_config])
     }