Revert "fix(ingest): Remove tsv-utils so that image can build on main (…

…#2185)" This reverts commit f076cc1.
loculus-project · Jul 3, 2024 · c447727 · c447727
1 parent 823ab18
commit c447727
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Showing 3 changed files with 5 additions and 73 deletions.
diff --git a/ingest/Snakefile b/ingest/Snakefile
@@ -148,21 +148,18 @@ rule align:
 
 rule process_alignments:
     input:
-        script="scripts/process_alignments.py",
         results=expand(
             "results/nextclade_{segment}.tsv",
             segment=config["nucleotide_sequences"],
         ),
     output:
         merged="results/nextclade_merged.tsv",
-    params:
-        log_level=LOG_LEVEL,
     shell:
         """
-        python {input.script} \
-            --input "{input.results}" \
-            --output {output.merged} \
-            --log-level {params.log_level} \
+        tsv-append --header {input.results} \
+        | tsv-select --header --fields seqName,clade \
+        | tsv-filter --header --not-empty clade \
+        > {output.merged}
         """
 
 

diff --git a/ingest/environment.yml b/ingest/environment.yml
@@ -18,4 +18,5 @@ dependencies:
   - requests
   - seqkit
   - snakemake
+  - tsv-utils
   - unzip
diff --git a/ingest/scripts/process_alignments.py b/ingest/scripts/process_alignments.py