fix(grz-common): meanReadLength param None vs 0 (#435)

tedil · web-flow · commit 90538aa6879b · 2025-10-23T09:29:41.000Z
For long read data, the mean read length check is ignored; the correct
respective parameter for grz-check is `0`, not `None`.
diff --git a/packages/grz-common/src/grz_common/workers/submission.py b/packages/grz-common/src/grz_common/workers/submission.py
@@ -244,7 +244,7 @@ def should_check_file(file_path: Path, file_metadata: File) -> bool:
                         lab_data.sequence_subtype,
                     )
                 ]
-                mean_read_length_threshold = thresholds.get("meanReadLength", None)
+                mean_read_length_threshold = thresholds.get("meanReadLength", 0)
 
                 sequence_data = lab_data.sequence_data
                 fastq_files = [f for f in sequence_data.files if f.file_type == FileType.fastq]

Original file line number	Diff line number	Diff line change
`@@ -244,7 +244,7 @@ def should_check_file(file_path: Path, file_metadata: File) -> bool:`
`244`	`244`	`lab_data.sequence_subtype,`
`245`	`245`	`)`
`246`	`246`	`]`
`247`		`- mean_read_length_threshold = thresholds.get("meanReadLength", None)`
	`247`	`+ mean_read_length_threshold = thresholds.get("meanReadLength", 0)`
`248`	`248`
`249`	`249`	`sequence_data = lab_data.sequence_data`
`250`	`250`	`fastq_files = [f for f in sequence_data.files if f.file_type == FileType.fastq]`