Ingest with nextclade

ingest/defaults/config.yaml

@@ -12,4 +12,6 @@ s3_dst:
   fauna: s3://nextstrain-data-private/files/workflows/avian-flu
 
 nextclade:
-  dataset_name: "community/moncla-lab/iav-h5/ha/all-clades"
+  dataset_name: community/moncla-lab/iav-h5/ha/all-clades
+  field_map: defaults/nextclade_field_map.tsv
+  id_field: seqName

ingest/defaults/nextclade_field_map.tsv

@@ -0,0 +1,28 @@
+# TSV file that is a mapping of column names for Nextclade output TSV
+# The first column should be the original column name of the Nextclade TSV
+# The second column should be the new column name to use in the final metadata TSV
+# Nextclade can have pathogen specific output columns so make sure to check which
+# columns would be useful for your downstream phylogenetic analysis.
+seqName	seqName
+clade	clade
+coverage	coverage
+totalMissing	missing_data
+totalSubstitutions	divergence
+totalNonACGTNs	nonACGTN
+qc.overallStatus	QC_overall
+qc.missingData.status	QC_missing_data
+qc.mixedSites.status	QC_mixed_sites
+qc.privateMutations.status	QC_rare_mutations
+qc.snpClusters.status	QC_snp_clusters
+qc.frameShifts.status	QC_frame_shifts
+qc.stopCodons.status	QC_stop_codons
+frameShifts	frame_shifts
+privateNucMutations.reversionSubstitutions	private_reversion_substitutions
+privateNucMutations.labeledSubstitutions	private_labeled_substitutions
+privateNucMutations.unlabeledSubstitutions	private_unlabeled_substitutions
+privateNucMutations.totalReversionSubstitutions	private_total_reversion_substitutions
+privateNucMutations.totalLabeledSubstitutions	private_total_labeled_substitutions
+privateNucMutations.totalUnlabeledSubstitutions	private_total_unlabeled_substitutions
+privateNucMutations.totalPrivateSubstitutions	private_total_private_substitutions
+qc.snpClusters.clusteredSNPs	private_snp_clusters
+qc.snpClusters.totalSNPs	private_total_snp_clusters

ingest/rules/merge_segment_metadata.smk

@@ -16,7 +16,7 @@ rule merge_segment_metadata:
         segments = expand("{{data_source}}/data/metadata_{segment}.tsv", segment=config["segments"]),
         metadata = "{data_source}/data/metadata_ha.tsv",
     output:
-        metadata = "{data_source}/results/metadata.tsv",
+        metadata = "{data_source}/data/merged_segment_metadata.tsv",
     shell:
         """
         python scripts/add_segment_counts.py \

ingest/rules/nextclade.smk

@@ -42,3 +42,39 @@ rule run_nextclade:
             --output-tsv {output.nextclade} \
             --output-fasta {output.alignment}
         """
+
+
+rule join_metadata_and_nextclade:
+    input:
+        nextclade="{data_source}/results/nextclade.tsv",
+        metadata="{data_source}/data/merged_segment_metadata.tsv",
+        nextclade_field_map=config["nextclade"]["field_map"],
+    output:
+        metadata="{data_source}/results/metadata.tsv",
+    params:
+        # Making this param optional because we don't have curate pipeline for fauna data
+        metadata_id_field=config.get("curate", {}).get("output_id_field", "strain"),
+        nextclade_id_field=config["nextclade"]["id_field"],
+    shell:
+        """
+        export SUBSET_FIELDS=`grep -v '^#' {input.nextclade_field_map} | awk '{{print $1}}' | tr '\n' ',' | sed 's/,$//g'`
+
+        csvtk fix-quotes -t {input.nextclade} \
+        | csvtk -t cut -f $SUBSET_FIELDS \
+        | csvtk -t rename2 \
+            -F \
+            -f '*' \
+            -p '(.+)' \
+            -r '{{kv}}' \
+            -k {input.nextclade_field_map} \
+        | csvtk del-quotes -t \
+        | 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}
+        """