fix: [tsv-join] Error processing command line arguments: Windows/DOS …

…line ending found for data/metadata_raw.tsv
nextstrain · Oct 4, 2023 · 7a704ff · 7a704ff
1 parent 3b2a1ec
commit 7a704ff
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/ingest/workflow/snakemake_rules/nextclade.smk b/ingest/workflow/snakemake_rules/nextclade.smk
@@ -74,13 +74,13 @@ rule join_metadata_clades:
 
         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 \
+        cat {input.metadata} | tr '\r' '\n' | grep -v "^$" \
+        | 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}
         """