From 50194209c1163d0d3e1f7dbe22a228fd7ce27258 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer <cornelius.roemer@gmail.com> Date: Wed, 20 Sep 2023 19:19:43 +0200 Subject: [PATCH] Undo defaults.yaml change, use one config per build, add default profile --- Snakefile | 4 --- config/config_hmpxv1.yaml | 16 +++++++++++ config/config_hmpxv1_big.yaml | 16 +++++++++++ config/config_mpxv.yaml | 23 ++++++++++++++++ config/defaults.yaml | 50 ----------------------------------- profiles/default/config.yaml | 5 ++++ 6 files changed, 60 insertions(+), 54 deletions(-) delete mode 100644 config/defaults.yaml create mode 100644 profiles/default/config.yaml diff --git a/Snakefile b/Snakefile index 0f1b2f66..60b06be7 100644 --- a/Snakefile +++ b/Snakefile @@ -11,10 +11,6 @@ if version.parse(augur_version) < version.parse(min_augur_version): sys.exit(1) -# Use default configuration values. Override with Snakemake's --configfile/--config options. -configfile: "config/defaults.yaml" - - build_dir = "results" diff --git a/config/config_hmpxv1.yaml b/config/config_hmpxv1.yaml index 807a9f38..489a0be9 100644 --- a/config/config_hmpxv1.yaml +++ b/config/config_hmpxv1.yaml @@ -1,5 +1,18 @@ +exclude: "config/exclude_accessions_mpxv.txt" +reference: "config/reference.fasta" +genemap: "config/genemap.gff" +genbank_reference: "config/reference.gb" colors: "config/colors_hmpxv1.tsv" +clades: "config/clades.tsv" +lat_longs: "config/lat_longs.tsv" auspice_config: "config/auspice_config_hmpxv1.json" +description: "config/description.md" +tree_mask: "config/tree_mask.tsv" + +# Use `accession` as the ID column since `strain` currently contains duplicates¹. +# ¹ https://github.com/nextstrain/monkeypox/issues/33 +strain_id_field: "accession" +display_strain_field: "strain" build_name: "hmpxv1" auspice_name: "mpox_mpxv-IIb" @@ -58,6 +71,9 @@ root: "MK783032 MK783030" clock_rate: 5.7e-5 clock_std_dev: 2e-5 +## recency +recency: true + mask: from_beginning: 800 from_end: 6422 diff --git a/config/config_hmpxv1_big.yaml b/config/config_hmpxv1_big.yaml index ced85742..6fba0745 100644 --- a/config/config_hmpxv1_big.yaml +++ b/config/config_hmpxv1_big.yaml @@ -1,5 +1,18 @@ +exclude: "config/exclude_accessions_mpxv.txt" +reference: "config/reference.fasta" +genemap: "config/genemap.gff" +genbank_reference: "config/reference.gb" colors: "config/colors_hmpxv1.tsv" +clades: "config/clades.tsv" +lat_longs: "config/lat_longs.tsv" auspice_config: "config/auspice_config_hmpxv1_big.json" +description: "config/description.md" +tree_mask: "config/tree_mask.tsv" + +# Use `accession` as the ID column since `strain` currently contains duplicates¹. +# ¹ https://github.com/nextstrain/monkeypox/issues/33 +strain_id_field: "accession" +display_strain_field: "strain" build_name: "hmpxv1_big" auspice_name: "mpox_mpxv-IIb-B.1" @@ -36,6 +49,9 @@ root: "OP890401" clock_rate: 5.7e-5 clock_std_dev: 2e-5 +## recency +recency: true + mask: from_beginning: 800 from_end: 6422 diff --git a/config/config_mpxv.yaml b/config/config_mpxv.yaml index 5447e329..168c56fd 100644 --- a/config/config_mpxv.yaml +++ b/config/config_mpxv.yaml @@ -1,5 +1,18 @@ +exclude: "config/exclude_accessions_mpxv.txt" +reference: "config/reference.fasta" +genemap: "config/genemap.gff" +genbank_reference: "config/reference.gb" colors: "config/colors_mpxv.tsv" +lat_longs: "config/lat_longs.tsv" auspice_config: "config/auspice_config_mpxv.json" +description: "config/description.md" +clades: "config/clades.tsv" +tree_mask: "config/tree_mask.tsv" + +# Use `accession` as the ID column since `strain` currently contains duplicates¹. +# ¹ https://github.com/nextstrain/monkeypox/issues/33 +strain_id_field: "accession" +display_strain_field: "strain" build_name: "mpxv" auspice_name: "mpox_mpxv" @@ -41,12 +54,22 @@ filter: group_by: "--group-by country year" sequences_per_group: "--subsample-max-sequences 100" +## align +max_indel: 10000 +seed_spacing: 1000 + +## treefix +fix_tree: true + ## refine timetree: false root: "min_dev" clock_rate: 3e-6 clock_std_dev: 6e-6 +## recency +recency: true + mask: from_beginning: 1350 from_end: 6422 diff --git a/config/defaults.yaml b/config/defaults.yaml deleted file mode 100644 index 7d685a22..00000000 --- a/config/defaults.yaml +++ /dev/null @@ -1,50 +0,0 @@ -# This configuration file contains all required configuration entries with -# hmpxv1-focused default values. -# Use Snakemake's --configfile/--config options to override default values. - -exclude: "config/exclude_accessions_mpxv.txt" -reference: "config/reference.fasta" -genemap: "config/genemap.gff" -genbank_reference: "config/reference.gb" -colors: "config/colors_hmpxv1.tsv" -clades: "config/clades.tsv" -lat_longs: "config/lat_longs.tsv" -auspice_config: "config/auspice_config_hmpxv1.json" -description: "config/description.md" -tree_mask: "config/tree_mask.tsv" - -# Use `accession` as the ID column since `strain` currently contains duplicates¹. -# ¹ https://github.com/nextstrain/monkeypox/issues/33 -strain_id_field: "accession" -display_strain_field: "strain" - -build_name: "default_hmpxv1" -auspice_name: "default_hmpxv1" - -## filter -min_date: 2017 -min_length: 100000 -sequences_per_group: "--sequences-per-group 40" -group_by: "--group-by year month country" -filters: "--exclude-where outbreak!=hMPXV-1" - -## align -max_indel: 10000 -seed_spacing: 1000 - -## treefix -fix_tree: true - -## refine -timetree: true -root: "MK783032 MK783030" -clock_rate: 5.7e-5 -clock_std_dev: 2e-5 - -## recency -recency: true - -mask: - from_beginning: 800 - from_end: 6422 - maskfile: "config/mask.bed" diff --git a/profiles/default/config.yaml b/profiles/default/config.yaml new file mode 100644 index 00000000..4f554b22 --- /dev/null +++ b/profiles/default/config.yaml @@ -0,0 +1,5 @@ +cores: all +printshellcmds: true +reason: true +rerun-incomplete: true +configfile: config/config_mpxv.yaml