move checkpoint

Author: bpblanken

v03_pipeline/lib/reference_datasets/splice_ai.py

@@ -9,12 +9,12 @@ def get_ht(
     paths: list[str],
     reference_genome: ReferenceGenome,
 ) -> hl.Table:
-    ht = vcf_to_ht(paths, reference_genome)
-
     # NB: We ran into weird issues...running out
     # of file descriptors on dataproc :/
-    ht, _ = checkpoint(ht)
     hl._set_flags(use_new_shuffle=None, no_whole_stage_codegen='1')  # noqa: SLF001
+    ht = vcf_to_ht(paths, reference_genome)
+    ht, _ = checkpoint(ht)
+
 
     # SpliceAI INFO field description from the VCF header: SpliceAIv1.3 variant annotation. These include
     # delta scores (DS) and delta positions (DP) for acceptor gain (AG), acceptor loss (AL), donor gain (DG), and