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Merge pull request #1 from nextstrain/update_ingest
Update ingest to accommodate oropouche segments
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@@ -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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>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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