Replace join metadata and clades script with csvtk and tsv append

As part of centralizing ingest scripts, replace the join-metadata-and-clades.py
script with csvtk and tsv append when there aren't any customized calculations.

nextstrain/ingest#23

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

@@ -0,0 +1,17 @@
+key	value
+index	index
+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

@@ -56,15 +56,31 @@ rule join_metadata_clades:
     input:
         nextclade="data/nextclade.tsv",
         metadata="data/metadata_raw.tsv",
+        nextclade_field_map="source-data/nextclade-field-map.tsv",
     output:
-        "data/metadata.tsv",
+        metadata="data/metadata.tsv",
     params:
         id_field=config["transform"]["id_field"],
     shell:
         """
-        python3 bin/join-metadata-and-clades.py \
-                --id-field {params.id_field} \
-                --metadata {input.metadata} \
-                --nextclade {input.nextclade} \
-                -o {output}
+        csvtk -tl rename2 \
+            -F \
+            -f '*' \
+            -p '(.+)' \
+            -r '{{kv}}' \
+            -k {input.nextclade_field_map} \
+            {input.nextclade} \
+            > results/nextclade_renamed.tsv
+
+        export APPEND_FIELDS=`awk 'NR>1 {{print $2}}' {input.nextclade_field_map} | grep -v -e "index" -e "seqName" | tr '\n' ',' | sed 's/,\$//g'`
+
+        tsv-join -H \
+            --filter-file results/nextclade_renamed.tsv \
+            --key-fields seqName \
+            --data-fields {params.id_field} \
+            --append-fields $APPEND_FIELDS \
+            --allow-duplicate-keys \
+            --write-all ? \
+            {input.metadata} \
+            > {output.metadata}
         """