Sort bowtie2 outputs for reproducibility

[rzlim08]

• This PR attempts to make almost all outputs of the short-read-mngs pipeline reproducible when run on the same input.
• The changes made here are issues in sorting:
  1. sort bowtie2_ercc.sam file
  2. sort bowtie2 output from reads to contig mapping
  3. sort list of NT/NR source in output json

The outputs were tested as following:

1. Run 2 pipelines with the same input
2. Run python3 scripts/compare-outputs.py <output.json> <output2.json> to compare md5 hashes
3. Manually diff files to determine the cause of the discrepancies

The remaining files which are different on every run are: czid_short_read_mngs.host_filter.fastp_html czid_short_read_mngs.postprocess.assembly_out_assembly_spades_output_log

Both of which contain timestamps which account for the discrepancy

[katrinakalantar]

This looks good to me too! Thanks for making these changes!