Ensure index files are stored under the same dir/bucket as their respective file in EH WDL

[VJalili]

If a BAM/CRAM file and its respective index are stored under a different bucket, they will be localized to different paths on the runner. However, EH requires a BAM/CRAM and its respective index stored under the same path. This PR ensures the files are stored under the same path. The same applied to reference files.

The implemented approach preserves .bam or .cram extension. One another alternative could be the following.

BAM_OR_CRAM=~{bam_or_cram}
EXT="${BAM_OR_CRAM##*.}"
if [ $EXT == "bam" ]; then
    BAM_OR_CRAM="~{sample_id}".bam
    BAM_OR_CRAM_INDEX="~{sample_id}".bam.bai
else
    BAM_OR_CRAM="~{sample_id}".cram
    BAM_OR_CRAM_INDEX="~{sample_id}".cram.crai
fi
mv ~{bam_or_cram} BAM_OR_CRAM
mv ~{bam_or_cram_index} BAM_OR_CRAM_INDEX

[mwalker174]

LGTM, one minor question.

[mwalker174]

Do you need the if?

[VJalili]

in my tests, mv exits with fail code if the file is already there.

[VJalili]

@mwalker174 Thanks for reviewing this!