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Merge pull request #1 from nextstrain/update_ingest
Update ingest to accommodate oropouche segments
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,95 +1,54 @@ | ||
| """ | ||
| This part of the workflow handles running Nextclade on the curated metadata | ||
| and sequences. | ||
| and sequences to split the sequences into L, M, and S segments. | ||
| REQUIRED INPUTS: | ||
| metadata = data/subset_metadata.tsv | ||
| sequences = results/sequences.fasta | ||
| metadata = data/subset_metadata.tsv | ||
| all_metadata = results/all/metadata.tsv | ||
| sequences = results/all/sequences.fasta | ||
| OUTPUTS: | ||
| metadata = results/metadata.tsv | ||
| nextclade = results/nextclade.tsv | ||
| alignment = results/alignment.fasta | ||
| translations = results/translations.zip | ||
| metadata = results/{segment}/metadata.tsv | ||
| sequences = results/{segment}/sequences.fasta | ||
| See Nextclade docs for more details on usage, inputs, and outputs if you would | ||
| like to customize the rules: | ||
| https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli.html | ||
| """ | ||
| DATASET_NAME = config["nextclade"]["dataset_name"] | ||
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| rule get_nextclade_dataset: | ||
| """Download Nextclade dataset""" | ||
| output: | ||
| dataset=f"data/nextclade_data/{DATASET_NAME}.zip", | ||
| params: | ||
| dataset_name=DATASET_NAME | ||
| shell: | ||
| """ | ||
| nextclade3 dataset get \ | ||
| --name={params.dataset_name:q} \ | ||
| --output-zip={output.dataset} \ | ||
| --verbose | ||
| """ | ||
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| rule run_nextclade: | ||
| rule run_nextclade_to_identify_segment: | ||
| input: | ||
| dataset=f"data/nextclade_data/{DATASET_NAME}.zip", | ||
| sequences="results/sequences.fasta", | ||
| sequences = "results/all/sequences.fasta", | ||
| segment_reference = config["nextclade"]["segment_reference"], | ||
| output: | ||
| nextclade="results/nextclade.tsv", | ||
| alignment="results/alignment.fasta", | ||
| translations="results/translations.zip", | ||
| sequences = "results/{segment}/sequences.fasta", | ||
| 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: "results/translations/{cds}.fasta", | ||
| min_seed_cover = config["nextclade"]["min_seed_cover"], | ||
| shell: | ||
| """ | ||
| nextclade3 run \ | ||
| {input.sequences} \ | ||
| --input-dataset {input.dataset} \ | ||
| --output-tsv {output.nextclade} \ | ||
| --output-fasta {output.alignment} \ | ||
| --output-translations {params.translations} | ||
| zip -rj {output.translations} results/translations | ||
| nextclade run \ | ||
| --input-ref {input.segment_reference} \ | ||
| --output-fasta {output.sequences} \ | ||
| --min-seed-cover {params.min_seed_cover} \ | ||
| --silent \ | ||
| {input.sequences} | ||
| """ | ||
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| rule join_metadata_and_nextclade: | ||
| rule subset_metadata_by_segment: | ||
| input: | ||
| nextclade="results/nextclade.tsv", | ||
| metadata="data/subset_metadata.tsv", | ||
| nextclade_field_map=config["nextclade"]["field_map"], | ||
| metadata = "results/all/metadata.tsv", | ||
| sequences = "results/{segment}/sequences.fasta", | ||
| output: | ||
| metadata="results/metadata.tsv", | ||
| metadata = "results/{segment}/metadata.tsv", | ||
| params: | ||
| metadata_id_field=config["curate"]["output_id_field"], | ||
| nextclade_id_field=config["nextclade"]["id_field"], | ||
| strain_id_field = config["curate"]["output_id_field"], | ||
| shell: | ||
| """ | ||
| export SUBSET_FIELDS=`grep -v '^#' {input.nextclade_field_map} | awk '{{print $1}}' | tr '\n' ',' | sed 's/,$//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.metadata_id_field} \ | ||
| --append-fields '*' \ | ||
| --write-all ? \ | ||
| {input.metadata} \ | ||
| | tsv-select -H --exclude {params.nextclade_id_field} \ | ||
| > {output.metadata} | ||
| """ | ||
| augur filter \ | ||
| --sequences {input.sequences} \ | ||
| --metadata {input.metadata} \ | ||
| --metadata-id-columns {params.strain_id_field} \ | ||
| --output-metadata {output.metadata} | ||
| """ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| >NC_005776.1 Oropouche virus segment L, complete genome | ||
| AGTAGTGTGCTCCTATTCCGAAACAAACAAAAACAATCTCAAAATGTCACAACTGTTGCTCAACCAATAT | ||
| CGGAATAGGATATTGCACTGCCGTGAACCTGAGATAGCAAAGGATATATGGCGAGATCTATTAAATGATC | ||
| GACACAATTACTTTTCTCGGGAATTTTGCAGAGCTGCAAATCTTGAGTACAGAAATGATGTTCCTGCTGA | ||
| GGATATTTGTGCTGAAGTTCTTGATGGTTATAAAGCAAGGAAAGTTCGCTTTTGTACACCTGATAATTAC | ||
| TTACTACATGATGGAAAGATGTATATAATAGACTTCAAAGTGTCTGTAGACGACCGATCTTCTAGAATCA | ||
| CAAGGGAGAAATATAATGAGATTTTTGGAGAGGTATTCAATCCAGAAGGTGTAGATTTTGAAATTGTTAT | ||
| TATTAGATTAGATCCTTCAAATATGACGATACATGTGGACTCTCGAGATTTCGTGAATACAATTGGGCCG | ||
| ATTACATTAAACATTAGTATGCAATGGTTTTTTGATATGAAAGACTTCTTGTTCGGGAAATTTCGGGATG | ||
| ATGATAAATTCCATGCTATAATAAGTCAAGGAGAATTCACAATGACATTGCCATGGATTGAAGAAGACAC | ||
| CCCAGAATTGCTTACTCATCCTATATACAATGAATTCATGAGTTCAATGCCAGAGGCAGAACAGGCCCTA | ||
| TTCAAGGAAGCATTGGAATTCAAATCATTTGGGGCAGAAAAATGGAATATCTTTTTGAAGGGGGTGATGT | ||
| CAAAGTATGGTGAATATTATAAAGAATTTACTAAAGGACATGCTCATTCTATATTTCTGACAACAGGGGA | ||
| CTACCCCAAGCCAGACAAAGACCAAATTTCAGCAGGTTGGAGAGAAATGGTAAACAGAGTAAGCTCTGAA | ||
| CGTGACATGTCAAATGACATAAATCAGGAAAAACCAAGCATGCATTTTATATGGGCAAAGAATGATTCAA | ||
| ATAGCAACAATAATATACAAAAGCTAATCAAACTATCTAAATCACTGCAAGCTATGAGCGGGACAGGGAG | ||
| CTATGTAAATGCTTTCAAGTCATTAGGGAGATTAATGGATATATCATCAGATGTTAAAAAATATGAATCA | ||
| TTTTGTGGGAAATTGAAATCTCTGGCAAGGTCTAGTATAAAAAAACTTGACAGGAAAATAGAGCCAATAC | ||
| AAATTGGGACTGCAACTGTCTTATGGGAACAGCAATTTAAACTAGATACAGATGTTATAAAAAGAGAAGA | ||
| CAGAATACATTTAATGAAAGATTATCTTGGGATCGGTAAGCACAAATCATTTTCAAAGAAATTAAACAAC | ||
| GACATAAATACTGATAAGCCTAAAATATTAAATTTCAACAATGATGATATAGTCAGGAAATGCAAAGATA | ||
| AATATAATCAAGTCATACATAACCTATCCCAAATCAATGAATTAGATAAGATTGGAAACTACCTAGAGCA | ||
| CTTTTCAGCTAAAATTAGTGCCTGCAGTGTAGAAATGTGGGATTTTATATATAATACAACCAAAACTAAA | ||
| TACTGGCAATGCATCAATGACTATTCCACCCTAATGAAAAACATGTTAGCTGTCTCTCAATATAATAGAC | ||
| ACAATACGTTTAGAATTGTCTCATGTGCAAACAATAATGTATTTGGTCTAGTAATGCCAAGCTCAGATAT | ||
| AAAGACAAAAAAAGCAACTTTAGTCTATGCAATAATGGCTCTCCATAATGAGGAGGCAGAAATAGCAGAA | ||
| CTTGGCTCACTCTACTCAACTTTTAAGACAGCAACAGGATATATTTCAATATCAAAGGCTTTTAGGCTGG | ||
| ATAAAGAAAGATGCCAACGCATAGTATCCTCTCCAGGCTTGTTCCTCATGACAAGCTGCCTATTATTCAA | ||
| CGGTAACAAGAGTTTAGAATTTGATAAATTACTAGGATTTTCATTTTTTACGTCAATATCAATTACGAAA | ||
| GCTATGCTCTCCCTTACTGAGCCTTCACGTTATATGATCATGAACTCGTTAGCAGTTTCCAGCCATGTAA | ||
| GAGAGTATATATCTGAAAAATTCTCCCCTTATACAAAAACATCATTTTCTGTGGTAATGACAGACTTAAT | ||
| CAAGAAGGGTTGCTATTCAGCATATGAACAGAGAAAAAAAGTACAAATAAGAGACATAAAATTAACAGAT | ||
| TATGATATAACACAAAAGGGAGTGGATTCCAAAAGAGATCTTAAATCTATTTGGTTCCCAGGAAAGGTAA | ||
| ACCTGAAAGAATATTTAAACCAAATTTATCTACCATTTTATTTTAACTCTAAAGGATTACATGAAAAACA | ||
| TCATGTCTTGATAGATTTGGCTAAAACAGTACTAGAAATCGAAAAAGAGCAAAGGGAGTCATTACCTGAG | ||
| CCATGGTCAGAGATACCTGCTAAGCGACTGTCACTTAATGTTTTAATTTACTCATTGCAGGAACTGAATT | ||
| TAGATACTTCAAGACATAATTTTGTAAGAAGCCGGGTGGAAAACGCAAATAATTTCAACAGATCTATAAC | ||
| GACAATATCTACTTTTACCAGCTCAAAATCATGCATTAAGATTGGTGATTTTGAAGAAGAAAAAAGAGAA | ||
| AAACTAAGAATGATACAAAAGAAACTTGCAAAGGATATTTCTAAATTAACCATAGCCAACCCAGCATTCT | ||
| TAGATGAGATCACAAACGAACATGAGATAAGGCATTCAACTTATGAGGACTTAAAACAATCTATCCCAGA | ||
| TTACACAGATTATATGTCTGTGAAAGTTTTTGACAGATTGTACGAGAAGATTACTACCAATGAAATAAAT | ||
| GATAAGGAAACAGTCAAGCTGATTCTAGAGACCATGAAAAAACATAAAATATTTCATTTTGGATTCTTCA | ||
| ATAAAGGACAAAAAACAGCCAAAGATAGAGAAATATTTTTAGGTGAATTTGAAGCAAAAATGTGTCTGTA | ||
| CCTTGTCGAAAGAATAGCTAAAGAGAGGTGCAAATTAAACCCTGAAGAAATGATAAGTGAACCAGGCGAC | ||
| TCGAAACTAAGGGTATTAGAGAAGCAATCAGAAGACGAAATCAGGTATATTAGCAATACAATAAAGACAT | ||
| TAGGGAATGCCATAGAGAACTTGCAATCTGGATCTTTAAATTGGGCAGATATATGCGAAAACAAAGCAAG | ||
| AGGACTTAAGATAGAAATAAATGCTGATATGTCCAAATGGAGTGCCCAAGATGTACTTTTTAAATATTTT | ||
| TGGTTGATAGTGCTTGATCCCATCTTATATCCTGCTGAGAGGAAAAGGATAATTTATTTCCTCTGTAATT | ||
| ATATGCAGAAAAGGCTTATAATGCCCGATGAATTGCTCACTACTATATTGGATCAAAGAGTTCCTTATTC | ||
| AAATGACATAATTGGATTAATGACAAACAATTATAGGTCTAATACAGTAGAAATAAAGCGTAACTGGCTT | ||
| CAAGGCAACTTAAATTATACAAGCAGTTACTTACACAGCTGTAGTATGTCTGTGTACAAAGATATAATAA | ||
| GAGAAGCAGCAATATTATTAGAAGGAGAAGCCCTTGTGAACTCAATGGTACATTCTGATGATAATCAAAC | ||
| ATCTATATGTATGGTGCAGAATAAATTACCAGATGACAATATAATTGAATTTTGCATTAAGATATTCGAG | ||
| AAGATATGCTTAACTTTTGGCAATCAGGCAAATATGAAGAAGACATATCTAACTAACTTCATCAAAGAGT | ||
| TTGTTTCTTTATTTAATATACATGGAGAACCATTTTCTATATATGGGAGATTTCTACTCACAGCAGTAGG | ||
| AGACTGTGCCTATCTAGGGCCTTATGAAGATTTAGCAAGTAGGCTATCTGCAACACAAACTGCTATAAAG | ||
| CATGGTTGCCCACCATCACTTGCATGGGTATCTATCGCTCTAAATCACTGGATAACCCACACTACATATA | ||
| ATATGTTGCCTGGCCAAAATAATGACCCGTTACCATTCTTCCCTACTAACAATAGAAGTGAAATACCAGT | ||
| AGAGATGTGCGGAATACTAGAAAGTGATTTATCAACAATTGCACTAACTGGTTTAGAAGCAGGGAATGTC | ||
| ACGTTTCTAACAAATATAGCAAGGAAGTTATCATCCCCAATCTTACAAAGAGAAAGTATTCAAGATCAAT | ||
| ACAATTCTATAGAAAAGTGGGATCTGAGCAAATTATCACAGATCGACATTCTAAGGCTTAAAATGCTCAG | ||
| GTATATATCTCTTGATAGTTCAGTCACATCTGATGATGGTATGGGGGAGACTAGTGAAATGAGATCTCGA | ||
| TCACTTTTAACACCTCGTAAATTCACAACAAGTGGGTCACTTAATAGGTTGAAATCATATAAAGACTTTC | ||
| AAGATATAATAGCAGATGAGGACAAGACAAACGAACTATTTGAGAATTTCATTAGACACCCAGAGTTACT | ||
| GGTTACAAAAGGCGAAACATTTGAAGAATTTGTTAATACGATATTATTTAGGTACAATTCAAAGAAATTC | ||
| AAAGAATCTTTGTCAATACAAAACCCAGCACAGCTTTTTATTGAGCAAATATTATTTTCCAATAAACCAG | ||
| TAATTGACTACACTAGCATACATGACAAGATTTTTGGATTACAAGACATGCCAGGAATTGAAGAACTAGA | ||
| TACAATTATAGGTCGCAAAACATTTGTTGAGAGTTATGTTCAAATCGTAGATGACTTAAGCAATTTAACA | ||
| TTGGATATAAACGATGTCAAGACTATATTTGCCTTTTGTCTTATGAATGACCCACTACTGATCACATCTG | ||
| CTAACAATATAATAATGTCTGTTAAGGGACATAGTCAAGAAAGAATAGGTCAATCAGCATGCAAAATGCC | ||
| AGAGGTCCGAAGTCTAAAACTCATACATTATTCACCAGCAGTTGTTTTGAGAGCCTATGTGAGAGGGCCA | ||
| ACAAATGTACCGAATGTAGATATAGATGAACTTGCAAGGGATCTATCTCATTTAGAAGACTTCATACAAA | ||
| GTACAAAACTCAGAGAAAATATGAGAGAGAGAATAGAAATAAATGAGAAGCGGCACTTAGGAAGGGATTT | ||
| CAAATTTGAAATCAAAGAACTAACTAGATTTTACCAAGTGTGTTATGATTACATAAAGTCTACAGAACAT | ||
| AAAGTCAAGGTATTCATATTGCCATACAAAGTTTTCACATCAATAGAATTCTGCGGGGCACTGACAGGTA | ||
| ACTTGATAAATGACAAATTATGGTACATAACGCATTATCTGAAAAATATAGTGTCTACTACACATAAGGC | ||
| ACAAATTTCTTCTTCACCTGAATTGGAATTGCAAATTGCTGATGAGGCACTAAGACTAGTAGCACATTTT | ||
| GCTGATACTTTCTTGGCATCAGAATCAAGAATACAATTTCTGAAGAAAATTATTGAAGAATTCACATACA | ||
| AAGGGATACCTGTAAAACATTTATACTCAAAAATAAAGAACTCCAAGTTGAGGGTTAAATTTCTAGGGAT | ||
| TCTTTTATGGTTAGATGATCTAACACAGAATGATCTGGATAAATTTGATGCAGATAAATCAGATGAAAAG | ||
| ATTATATGGAATAACTGGCAAGTGTCAAGAGATATGAATACTGGACCAATAGACTTAATGATAAGCGGTT | ||
| ACTCTAGACAGCTGCGGATCACTGGGGAAGATGACAAATTGATTGCTGCTGAATTGCAGGTTACTAGATT | ||
| GTCAGAAGATTTAATTTATAGACACGGTCAGGCAATGTTGAATAAGCCACACGGCTTAAAGCTTGAAAAA | ||
| ATGCAACCTGTGACTGAGATGTCTAAACGATTACATTATATCGTTTTCCAGCAAAGATCACGGAAACGAT | ||
| ACTTCTATTCTATATTACCCACCCAAGTAATTGAGGACCATAATTCTAGAGTTGAATCATCTAGGCTAAG | ||
| CAGAGATTCAAAATGGGTTCCTGTATGCCCTGTTGCAATATCAAAACTCTACCAACAAGGACGGCCTATA | ||
| CTTTCCAAAGTTAGAAATCTGAATATGCAGACTCATTCGCTTTCCAGAATACAAGTTAATGTAGATGAAT | ||
| ATGCCATCACGAGAAGAGCACATTTTCAGAAAATGCCTTTCTTCGAAGGACCATCAATCCCTTCTGGTGG | ||
| TATGGATTTGTCTGAGTTGATGAAATCTACATCCCTATTAAGCTTGAATTATGATAACATAAAAAATGCA | ||
| TCCTTATTGGACATGTCTAGGGTATTTAAGTGCAATGGCAGTGGAGATGACCAAATGGCTTTCGAATTTC | ||
| TATCGGACGAAATTTTGGAGCAAGATGTAGTTGAAGAAATAGAATGCAACCCTATATTTTCTATTAGTTA | ||
| TACAAAAAGAGGAGAATCCAATATGACTTATAAAAATGCTTTCCACAAAGCCTTAATCTCAGAATGTGAC | ||
| AAATTTGAAGAAGCATTTGACTTCCTCGACATGGGATTTTGCTCGAATGAAAATCTTAGTATTCTGGAGG | ||
| AAATACATTGGATAATCAGTTATTTAAAAACAAATCAATGGTCTACGGAACTAGACAATTGTATTCACAT | ||
| GTGCATGTACAGGAATGGATATGATGCAGAATATCATAAATTTGATATACCCTCTAAATTCCTCAAAGAC | ||
| CCAATAAACCGAACAATAAATTGGACTGAAGTCATTGAATTTATATTATTAATTGAAGATTTCCAAACAA | ||
| AAATTGAGCCATGGTCTAGTATGAAGTCACACTTCTGTTCAAAAGCACACAGTGTAGCACTAGAGTGTAT | ||
| GAAAAATGAGAAAAGATCATTGGCAGAATTTGTAGACAAAAGTAAGAAAACTGGCAAATCCAAATTTGAC | ||
| TTCTAAGGTATACACATGTAAAAGTAGTGTTTGTTTCTAAATAGGAGCACACTACT | ||
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