Bug #9485
closed
[bcbio] Changing truth vcf/bed prevents variant calling jobs being reused in bcbio cwl pipelines
Description
The cwl workflow generated by bcbio_vm.py has variant calling steps "batch_for_variantcall.cwl", "get_parallel_regions.cwl", and "variantcall_batch_region.cwl". They all have variables "config__algorithm__validate" and "config__algorithm__validate_regions" passed as inputs. If we change the truth vcf/bed, the cwl of these steps will change, preventing them being reused.
Is this the intended behavior?
Updated by Jiayong Li
Updated by Brad Chapman almost 8 years ago
You're right sorry for giving you the wrong answer on this before. The reason for this is that we pack the inputs into CWL records and then them all to the variant calling and validation steps. This allows parallelization and batching but would require a redo of steps in this sub-workflow if we change anu inputs. So unfortunately I don't have a way to work around it.
Updated by Tom Morris