Delete serotype nextclade dataset

ingest/workflow/snakemake_rules/nextclade.smk

@@ -1,75 +1,3 @@
-rule nextclade_all:
-    """
-    Classify sequences into DENV1, DENV2, DENV3, and DENV4
-    """
-    input:
-        sequences="data/sequences.fasta",
-        dataset="../nextclade_data/all",
-    output:
-        "data/nextclade_results/nextclade_all.tsv",
-    threads: 4
-    params:
-        min_length=1000,  # E gene length is approximately 1400
-        min_seed_cover=0.01,
-    shell:
-        """
-        nextclade run \
-          --input-dataset {input.dataset} \
-          -j {threads} \
-          --output-tsv {output} \
-          --min-seed-cover {params.min_seed_cover} \
-          --min-length {params.min_length} \
-          --silent \
-          {input.sequences}
-        """
-
-# Might be able to parallelize this rule
-rule split_dengue_sequences:
-    """
-    Split sequences into DENV1, DENV2, DENV3, and DENV4
-    """
-    input:
-        sequences="data/sequences.fasta",
-        metadata="data/metadata.tsv",
-        nextclade_all_results="data/nextclade_results/nextclade_all.tsv",
-    output:
-        sequences_all="results/sequences_all.fasta",
-        sequences_denv1="results/sequences_denv1.fasta",
-        sequences_denv2="results/sequences_denv2.fasta",
-        sequences_denv3="results/sequences_denv3.fasta",
-        sequences_denv4="results/sequences_denv4.fasta",
-    shell:
-        """
-        cp {input.sequences} {output.sequences_all}
-        
-        augur filter \
-          --sequences {input.sequences} \
-          --metadata {input.nextclade_all_results} \
-          --metadata-id-columns seqName \
-          --query "clade=='DENV1'" \
-          --output-sequences {output.sequences_denv1}
-        
-        augur filter \
-          --sequences {input.sequences} \
-          --metadata {input.nextclade_all_results} \
-          --metadata-id-columns seqName \
-          --query "clade=='DENV2'" \
-          --output-sequences {output.sequences_denv2}
-
-        augur filter \
-          --sequences {input.sequences} \
-          --metadata {input.nextclade_all_results} \
-          --metadata-id-columns seqName \
-          --query "clade=='DENV3'" \
-          --output-sequences {output.sequences_denv3}
-
-        augur filter \
-          --sequences {input.sequences} \
-          --metadata {input.nextclade_all_results} \
-          --metadata-id-columns seqName \
-          --query "clade=='DENV4'" \
-          --output-sequences {output.sequences_denv4}
-        """
 
 rule nextclade_denvX:
     """

nextclade_data/README.md

@@ -2,7 +2,6 @@
 
 | Serotype | Reference | Nextclade link |
 |:--|:--|:--|
-| all | [NC_002640.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_002640.1) | [nextclade all](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/dengue/tree/main/nextclade_data/all) |
 | denv1 | [NC_001477.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_001477.1) | [nextclade denv1](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/dengue/tree/main/nextclade_data/denv1) |
 | denv2 | [NC_001474.2](https://www.ncbi.nlm.nih.gov/nuccore/NC_001474.2) | [nextclade denv2](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/dengue/tree/main/nextclade_data/denv2) |
 | denv3 | [NC_001475.2](https://www.ncbi.nlm.nih.gov/nuccore/NC_001475.2) | [nextclade denv3](https://clades.nextstrain.org/?dataset-url=https://github.com/nextstrain/dengue/tree/main/nextclade_data/denv3) |