Re add nextclade assignment rules

ingest/Snakefile

@@ -57,6 +57,7 @@ rule all:
 
 include: "workflow/snakemake_rules/fetch_sequences.smk"
 include: "workflow/snakemake_rules/transform.smk"
+include: "workflow/snakemake_rules/nextclade.smk"
 
 
 if config.get("upload", False):

ingest/source-data/nextclade-field-map.tsv

@@ -0,0 +1,16 @@
+key	value
+seqName	seqName
+clade	clade
+outbreak	outbreak
+lineage	lineage
+coverage	coverage
+totalMissing	missing_data
+totalSubstitutions	divergence
+totalNonACGTNs	nonACGTN
+qc.missingData.status	QC_missing_data
+qc.mixedSites.status	QC_mixed_sites
+qc.privateMutations.status	QC_rare_mutations
+qc.frameShifts.status	QC_frame_shifts
+qc.stopCodons.status	QC_stop_codons
+frameShifts	frame_shifts
+isReverseComplement	is_reverse_complement

ingest/workflow/snakemake_rules/nextclade.smk

@@ -0,0 +1,183 @@
+rule nextclade_all:
+    input:
+        sequences="results/sequences.fasta",
+        dataset="../nextclade_data/all",
+    output:
+        "results/nextclade_results/nextclade_all.tsv",
+    threads: 4
+    shell:
+        """
+        nextclade run \
+          --input-dataset {input.dataset} \
+          -j {threads} \
+          --output-tsv {output} \
+          --min-match-rate 0.01 \
+          --silent \
+          {input.sequences}
+        """
+
+# Might be able to parallelize this
+rule split_dengue_sequences:
+    input:
+        sequences="results/sequences.fasta",
+        metadata="results/metadata.tsv",
+        nextclade_all_results="results/nextclade_results/nextclade_all.tsv",
+    output:
+        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:
+        """
+        augur filter \
+          --sequences results/sequences.fasta
+          --metadata {input.nextclade_all_results} \
+          --metadata-id-columns seqName \
+          --query "clade=='DENV1'" \
+          --output-sequences {output.sequences_denv1}
+        
+        augur filter \
+          --sequences results/sequences.fasta
+          --metadata {input.nextclade_all_results} \
+          --metadata-id-columns seqName \
+          --query "clade=='DENV2'" \
+          --output-sequences {output.sequences_denv2}
+
+        augur filter \
+          --sequences results/sequences.fasta
+          --metadata {input.nextclade_all_results} \
+          --metadata-id-columns seqName \
+          --query "clade=='DENV3'" \
+          --output-sequences {output.sequences_denv3}
+
+        augur filter \
+          --sequences results/sequences.fasta
+          --metadata {input.nextclade_all_results} \
+          --metadata-id-columns seqName \
+          --query "clade=='DENV4'" \
+          --output-sequences {output.sequences_denv4}
+        """
+
+# The following rules should use wildcards
+rule nextclade_denv1:
+    input:
+        sequences="results/sequences_denv1.fasta",
+        dataset="../nextclade_data/denv1",
+    output:
+        "results/nextclade_results/nextclade_denv1.tsv",
+    threads: 4
+    shell:
+        """
+        nextclade run \
+          --input-dataset {input.dataset} \
+          -j {threads} \
+          --output-tsv {output} \
+          --min-match-rate 0.01 \
+          --silent \
+          {input.sequences}
+        """
+
+rule nextclade_denv2:
+    input:
+        sequences="results/sequences_denv2.fasta",
+        dataset="../nextclade_data/denv2",
+    output:
+        "results/nextclade_results/nextclade_denv2.tsv",
+    threads: 4
+    shell:
+        """
+        nextclade run \
+          --input-dataset {input.dataset} \
+          -j {threads} \
+          --output-tsv {output} \
+          --min-match-rate 0.01 \
+          --silent \
+          {input.sequences}
+        """
+
+rule nextclade_denv3:
+    input:
+        sequences="results/sequences_denv3.fasta",
+        dataset="../nextclade_data/denv3",
+    output:
+        "results/nextclade_results/nextclade_denv3.tsv",
+    threads: 4
+    shell:
+        """
+        nextclade run \
+          --input-dataset {input.dataset} \
+          -j {threads} \
+          --output-tsv {output} \
+          --min-match-rate 0.01 \
+          --silent \
+          {input.sequences}
+        """
+
+rule nextclade_denv4:
+    input:
+        sequences="results/sequences_denv4.fasta",
+        dataset="../nextclade_data/denv4",
+    output:
+        "results/nextclade_results/nextclade_denv4.tsv",
+    threads: 4
+    shell:
+        """
+        nextclade run \
+          --input-dataset {input.dataset} \
+          -j {threads} \
+          --output-tsv {output} \
+          --min-match-rate 0.01 \
+          --silent \
+          {input.sequences}
+        """
+
+#rule join_nextclade_clades:
+#    input:
+#        metadata="results/metadata.tsv",
+#        nextclade_denv1="results/nextclade_results/nextclade_denv1.tsv",
+#        nextclade_denv2="results/nextclade_results/nextclade_denv2.tsv",
+#        nextclade_denv3="results/nextclade_results/nextclade_denv3.tsv",
+#        nextclade_denv4="results/nextclade_results/nextclade_denv4.tsv",
+#    output:
+#        metadata_all="results/metadata_all.tsv",
+#        metadata_denv1="results/metadata_denv1.tsv",
+#        metadata_denv2="results/metadata_denv2.tsv",
+#        metadata_denv3="results/metadata_denv3.tsv",
+#        metadata_denv4="results/metadata_denv4.tsv",
+#    shell:
+#        """
+#        """
+
+
+# rule join_metadata_clades:
+#     input:
+#         nextclade="data/nextclade.tsv",
+#         metadata="data/metadata_raw.tsv",
+#         nextclade_field_map=config["nextclade"]["field_map"],
+#     output:
+#         metadata="results/metadata.tsv",
+#     params:
+#         id_field=config["transform"]["id_field"],
+#         nextclade_id_field=config["nextclade"]["id_field"],
+#     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}
+#         """