From ea71a787513f5356919ae162b87cebd3ba7935c4 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 18 Oct 2024 17:23:03 -0700 Subject: [PATCH 1/2] nextclade/export: Update REQUIRED INPUTS for Nextclade v3 Clarify the files required for `augur export` and the Nextclade v3 dataset files. --- nextclade/rules/export.smk | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/nextclade/rules/export.smk b/nextclade/rules/export.smk index aec5acb..ed8492b 100644 --- a/nextclade/rules/export.smk +++ b/nextclade/rules/export.smk @@ -4,19 +4,21 @@ export a reference tree and create the Nextclade dataset. REQUIRED INPUTS: - TODO: Confirm inputs for Nextclade v3 - reference = ../shared/reference.fasta - pathogen = config/pathogen.json - genome_annotation = config/genome_annotation.gff3 - readme = config/README.md - changelog = config/CHANGELOG.md - metadata = data/metadata.tsv - tree = results/tree.nwk - branch_lengths = results/branch_lengths.json - nt_muts = results/nt_muts.json - aa_muts = results/aa_muts.json - clades = results/clades.json - + augur export: + metadata = data/metadata.tsv + tree = results/tree.nwk + branch_lengths = results/branch_lengths.json + nt_muts = results/nt_muts.json + aa_muts = results/aa_muts.json + clades = results/clades.json + + Nextclade dataset files: + reference = ../shared/reference.fasta + pathogen = config/pathogen.json + genome_annotation = config/genome_annotation.gff3 + readme = config/README.md + changelog = config/CHANGELOG.md + example_sequences = config/sequence.fasta OUTPUTS: From 23d6072ca3f3c42cd7b37e869671e4c9e3478839 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 18 Oct 2024 17:25:46 -0700 Subject: [PATCH 2/2] nextclade/test-dataset: Update to `nextclade3` --- nextclade/build-configs/test-dataset/test_dataset.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextclade/build-configs/test-dataset/test_dataset.smk b/nextclade/build-configs/test-dataset/test_dataset.smk index d85aa5f..f0f3e98 100644 --- a/nextclade/build-configs/test-dataset/test_dataset.smk +++ b/nextclade/build-configs/test-dataset/test_dataset.smk @@ -12,7 +12,7 @@ rule test_dataset: dataset_dir="datasets/{build_name}", shell: """ - nextclade2 run \ + nextclade3 run \ {input.sequences} \ --input-dataset {params.dataset_dir} \ --output-all {output.outdir}