Casting the reference assembly to a string as b.read_input cannot par…

…se Posix
populationgenomics · Jul 23, 2024 · 59a025c · 59a025c
1 parent b6c2d61
commit 59a025c
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/cpg_workflows/jobs/align.py b/cpg_workflows/jobs/align.py
@@ -518,7 +518,7 @@ def extract_fastq(
     j.image(image_path('samtools'))
     # TODO: add ability to detect reference used in current BAM/CRAM and provide error handling
     if isinstance(alignment_input, CramPath | BamPath):
-        reference_path = b.read_input(alignment_input.reference_assembly)
+        reference_path = b.read_input(str(alignment_input.reference_assembly))
     else:
         reference_path = fasta_res_group(b)['base']
     res = STANDARD.request_resources(ncpu=16)