As part of the ticket to process SS2 data from HCA data browser in Terra, we need to accept fastq inputs that are not named with the .fastq.gz extension. Since the HISAT2 tool requires this file extension for internal validation, we must rename files if the extension is not present. The paired end version of this command was already doing this, but single-end was missing this step.
Changes
This adds the check to the single-end hisat2 call to check input fastq file name ends in .fastq.gz and rename the file if needed.
Purpose
.fastq.gzextension. Since the HISAT2 tool requires this file extension for internal validation, we must rename files if the extension is not present. The paired end version of this command was already doing this, but single-end was missing this step.Changes
.fastq.gzand rename the file if needed.Review Instructions