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Merge pull request #281 from nextstrain/ingest-nextclade-v3
Migrate to Nextclade v3
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,86 +1,115 @@ | ||
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| rule nextclade_dataset: | ||
| output: | ||
| temp("mpxv.zip"), | ||
| shell: | ||
| """ | ||
| nextclade2 dataset get --name MPXV --output-zip {output} | ||
| """ | ||
| import sys | ||
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| rule nextclade_dataset_hMPXV: | ||
| rule get_nextclade_dataset: | ||
| output: | ||
| temp("hmpxv.zip"), | ||
| temp("data/mpxv.zip"), | ||
| params: | ||
| dataset_name="MPXV", | ||
| log: | ||
| "logs/get_nextclade_dataset.txt", | ||
| benchmark: | ||
| "benchmarks/get_nextclade_dataset.txt" | ||
| shell: | ||
| """ | ||
| nextclade2 dataset get --name hMPXV --output-zip {output} | ||
| r""" | ||
| nextclade3 dataset get \ | ||
| --name {params.dataset_name:q} \ | ||
| --output-zip {output:q} 2>&1 | tee {log} | ||
| """ | ||
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| rule align: | ||
| rule run_nextclade: | ||
| input: | ||
| sequences="results/sequences.fasta", | ||
| dataset="hmpxv.zip", | ||
| dataset="data/mpxv.zip", | ||
| output: | ||
| alignment="data/alignment.fasta", | ||
| insertions="data/insertions.csv", | ||
| translations="data/translations.zip", | ||
| nextclade="results/nextclade.tsv", | ||
| alignment="results/alignment.fasta", | ||
| translations="results/translations.zip", | ||
| params: | ||
| # The lambda is used to deactivate automatic wildcard expansion. | ||
| # https://github.com/snakemake/snakemake/blob/384d0066c512b0429719085f2cf886fdb97fd80a/snakemake/rules.py#L997-L1000 | ||
| translations=lambda w: "data/translations/{gene}.fasta", | ||
| threads: 4 | ||
| translations=lambda w: "results/translations/{cds}.fasta", | ||
| threads: workflow.cores | ||
| log: | ||
| "logs/run_nextclade.txt", | ||
| benchmark: | ||
| "benchmarks/run_nextclade.txt" | ||
| shell: | ||
| """ | ||
| nextclade2 run -D {input.dataset} -j {threads} --retry-reverse-complement \ | ||
| --output-fasta {output.alignment} --output-translations {params.translations} \ | ||
| --output-insertions {output.insertions} {input.sequences} | ||
| zip -rj {output.translations} data/translations | ||
| r""" | ||
| nextclade3 run \ | ||
| {input.sequences:q} \ | ||
| --jobs {threads:q} \ | ||
| --retry-reverse-complement \ | ||
| --input-dataset {input.dataset:q} \ | ||
| --output-tsv {output.nextclade:q} \ | ||
| --output-fasta {output.alignment:q} \ | ||
| --output-translations {params.translations:q} 2>&1 | tee {log} | ||
| zip -rj {output.translations:q} results/translations | ||
| """ | ||
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| rule nextclade: | ||
| if isinstance(config["nextclade"]["field_map"], str): | ||
| print( | ||
| f"Converting config['nextclade']['field_map'] from TSV file ({config['nextclade']['field_map']}) to dictionary; " | ||
| f"consider putting the field map directly in the config file.", | ||
| file=sys.stderr, | ||
| ) | ||
| with open(config["nextclade"]["field_map"], "r") as f: | ||
| config["nextclade"]["field_map"] = dict( | ||
| line.rstrip("\n").split("\t", 1) for line in f if not line.startswith("#") | ||
| ) | ||
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| rule nextclade_metadata: | ||
| input: | ||
| sequences="results/sequences.fasta", | ||
| dataset="mpxv.zip", | ||
| nextclade="results/nextclade.tsv", | ||
| output: | ||
| "data/nextclade.tsv", | ||
| threads: 4 | ||
| nextclade_metadata=temp("results/nextclade_metadata.tsv"), | ||
| params: | ||
| nextclade_id_field=config["nextclade"]["id_field"], | ||
| nextclade_field_map=[ | ||
| f"{old}={new}" for old, new in config["nextclade"]["field_map"].items() | ||
| ], | ||
| nextclade_fields=",".join(config["nextclade"]["field_map"].keys()), | ||
| log: | ||
| "logs/nextclade_metadata.txt", | ||
| benchmark: | ||
| "benchmarks/nextclade_metadata.txt" | ||
| shell: | ||
| """ | ||
| nextclade2 run -D {input.dataset} -j {threads} --output-tsv {output} {input.sequences} --retry-reverse-complement | ||
| r""" | ||
| (tsv-select --header --fields {params.nextclade_fields:q} {input.nextclade} \ | ||
| | augur curate rename \ | ||
| --metadata - \ | ||
| --id-column {params.nextclade_id_field:q} \ | ||
| --field-map {params.nextclade_field_map:q} \ | ||
| --output-metadata {output.nextclade_metadata:q} ) 2>&1 | tee {log} | ||
| """ | ||
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| rule join_metadata_clades: | ||
| rule join_metadata_and_nextclade: | ||
| input: | ||
| nextclade="data/nextclade.tsv", | ||
| metadata="data/subset_metadata.tsv", | ||
| nextclade_field_map=config["nextclade"]["field_map"], | ||
| nextclade_metadata="results/nextclade_metadata.tsv", | ||
| output: | ||
| metadata="results/metadata.tsv", | ||
| params: | ||
| id_field=config["curate"]["id_field"], | ||
| metadata_id_field=config["curate"]["id_field"], | ||
| nextclade_id_field=config["nextclade"]["id_field"], | ||
| log: | ||
| "logs/join_metadata_and_nextclade.txt", | ||
| benchmark: | ||
| "benchmarks/join_metadata_and_nextclade.txt" | ||
| shell: | ||
| """ | ||
| export SUBSET_FIELDS=`awk 'NR>1 {{print $1}}' {input.nextclade_field_map} | tr '\n' ',' | sed 's/,$//g'` | ||
| csvtk -tl cut -f $SUBSET_FIELDS \ | ||
| {input.nextclade} \ | ||
| | csvtk -tl rename2 \ | ||
| -F \ | ||
| -f '*' \ | ||
| -p '(.+)' \ | ||
| -r '{{kv}}' \ | ||
| -k {input.nextclade_field_map} \ | ||
| | tsv-join -H \ | ||
| --filter-file - \ | ||
| --key-fields {params.nextclade_id_field} \ | ||
| --data-fields {params.id_field} \ | ||
| --append-fields '*' \ | ||
| --write-all ? \ | ||
| {input.metadata} \ | ||
| | tsv-select -H --exclude {params.nextclade_id_field} \ | ||
| > {output.metadata} | ||
| r""" | ||
| augur merge \ | ||
| --metadata \ | ||
| metadata={input.metadata:q} \ | ||
| nextclade={input.nextclade_metadata:q} \ | ||
| --metadata-id-columns \ | ||
| metadata={params.metadata_id_field:q} \ | ||
| nextclade={params.nextclade_id_field:q} \ | ||
| --output-metadata {output.metadata:q} \ | ||
| --no-source-columns 2>&1 | tee {log} | ||
| """ |
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