We are now pulling NCBI SRA data from s3. When we go to determine the transcriptome index length to process these files we need to use sra-stat to read the file. In order for that code path to execute we need to ensure that we define sra_file_input_path.
Note: I think it would be better instead of looking at the download source, to instead inspect the file to determine its type before determining index length.
Methods
n/a
Types of changes
Bugfix (non-breaking change which fixes an issue)
Functional tests
n/a tested locally
Checklist
[X] Lint and unit tests pass locally with my changes
Issue Number
N/A
Purpose/Implementation Notes
We are now pulling NCBI SRA data from s3. When we go to determine the transcriptome index length to process these files we need to use
sra-statto read the file. In order for that code path to execute we need to ensure that we definesra_file_input_path.Note: I think it would be better instead of looking at the download source, to instead inspect the file to determine its type before determining index length.
Methods
n/a
Types of changes
Functional tests
n/a tested locally
Checklist
Screenshots
N/A