fixup tests

workflows/short-read-mngs/auto_benchmark/harvest.py

@@ -93,7 +93,7 @@ def harvest_sample(sample, outputs_json, taxadb):
         outputs_json["czid_short_read_mngs.host_filter.fastp_out_fastp2_fastq"]
         is not None
     )
-    ans["input_reads"] = read_output_jsonfile(outputs_json, "host_filter.input_read_count")[
+    ans["input_reads"] = read_output_jsonfile(outputs_json, "host_filter.reads_in_count")[
         "fastqs"
     ]
     for step in [

workflows/short-read-mngs/test/host_filter/test_RunCZIDDedup.py

@@ -28,7 +28,7 @@ def test_RunCZIDDedup_safe_csv(util, short_read_mngs_bench3_viral_outputs):
         input_file.seek(0)
         assert special_char_rows == quote_count
 
-        inputs["reads1_fastq"] = [input_file.name]
+        inputs["reads1_fastq"] = input_file.name
 
         outp = util.miniwdl_run(
             util.repo_dir() / "workflows/short-read-mngs/host_filter.wdl",