From 785e8a02e37d790bea8b07f69a7c7d1cb6bfd324 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Tue, 10 Oct 2023 13:55:17 +0000 Subject: [PATCH 1/2] add dummy files for colors and genes --- workflows/phylogenetics/wf_augur.wdl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/phylogenetics/wf_augur.wdl b/workflows/phylogenetics/wf_augur.wdl index 1e209c698..73a81ca1c 100644 --- a/workflows/phylogenetics/wf_augur.wdl +++ b/workflows/phylogenetics/wf_augur.wdl @@ -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 @@ -39,6 +37,8 @@ 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 +112,7 @@ 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]), + 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) @@ -126,7 +126,7 @@ 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, @@ -150,7 +150,7 @@ workflow augur { augur_clades.clade_assignments_json, augur_traits.traits_assignments_json]), build_name = build_name, - colors_tsv = select_first([colors, mpxv_defaults.colors]), + 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]) } From 2a43d01bd34b6569a58d264f9100c402616b256c Mon Sep 17 00:00:00 2001 From: jrotieno Date: Tue, 10 Oct 2023 14:22:57 +0000 Subject: [PATCH 2/2] fix augur optional inputs (colors and genes) causing errors when running mpxv --- tasks/utilities/task_augur_utilities.wdl | 4 ---- workflows/phylogenetics/wf_augur.wdl | 4 ---- 2 files changed, 8 deletions(-) diff --git a/tasks/utilities/task_augur_utilities.wdl b/tasks/utilities/task_augur_utilities.wdl index ec85e1581..30fc45fcc 100644 --- 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 index 73a81ca1c..fcf95567f 100644 --- 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]) }