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Update nextclade workflow docs for v3 #70

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merged 2 commits into from
Oct 22, 2024
Merged

Update nextclade workflow docs for v3 #70

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ea71a78
nextclade/export: Update REQUIRED INPUTS for Nextclade v3
joverlee521 Oct 19, 2024
23d6072
nextclade/test-dataset: Update to `nextclade3`
joverlee521 Oct 19, 2024
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2 changes: 1 addition & 1 deletion nextclade/build-configs/test-dataset/test_dataset.smk
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Expand Up @@ -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}
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28 changes: 15 additions & 13 deletions nextclade/rules/export.smk
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Expand Up @@ -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:

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