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Remove the genes and colors input files #212

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merged 2 commits into from
Oct 11, 2023
Merged

Remove the genes and colors input files #212

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785e8a0
add dummy files for colors and genes
sage-wright Oct 10, 2023
2a43d01
fix augur optional inputs (colors and genes) causing errors when runn…
jrotieno Oct 10, 2023
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4 changes: 0 additions & 4 deletions tasks/utilities/task_augur_utilities.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
}
Expand All @@ -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
Expand Down
6 changes: 1 addition & 5 deletions workflows/phylogenetics/wf_augur.wdl
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Expand Up @@ -24,8 +24,6 @@ workflow augur {
String build_name
File? reference_fasta
File? reference_genbank
File? genes
File? colors
Int? min_num_unambig
String organism = "sars-cov-2" # options: sars-cov-2 or flu or mpxv
String flu_segment = "HA" # options: HA or NA
Expand Down Expand Up @@ -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([genes, mpxv_defaults.genes]),
build_name = build_name
}
if (flu_segment == "HA") { # we only have clade information for HA segments (but SC2 defaults will be selected first)
Expand All @@ -126,7 +123,7 @@ workflow augur {
}
}
if (! run_traits) {
if (defined(clades_tsv) || defined(sc2_defaults.clades_tsv) || defined(flu_defaults.clades_tsv) || defined(mpxv_defaults.clades_tsv) ) { # one of these must be present
if (defined(clades_tsv) || defined(sc2_defaults.clades_tsv) || defined(flu_defaults.clades_tsv) || defined(mpxv_defaults.clades_tsv)) { # one of these must be present
call clades_task.augur_clades { # assign clades to nodes based on amino-acid or nucleotide signatures
input:
refined_tree = augur_refine.refined_tree,
Expand All @@ -150,7 +147,6 @@ workflow augur {
augur_clades.clade_assignments_json,
augur_traits.traits_assignments_json]),
build_name = build_name,
colors_tsv = select_first([colors, mpxv_defaults.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])
}
Expand Down