Changing method of file name extraction

[RamiyapriyaS]

Description

Changed the method of file name extraction to include everything before "fastq.gz".

General Checks

• Have you run appropriate tests (unit/integration/end-to-end) to check logic across run environments (Conda/Docker/Singularity on Scicomp/AWS/NF Tower/Local)?

  For each relevant configuration:

  • Can the program run completely through without erroring out? Yes
  • Does it produce the expected outputs, given the inputs provided? Yes

[RamiyapriyaS]

Method of validation:

• Test the workflow with samples that include "dots" in the sample name (e.g. sample1.test.R1.fastq.gz, sample1.test.fasta)
• Test the workflow with existing test data that does not include "dots" in the sample name

[RamiyapriyaS]

Relevant issues: #252 and #173

[jessicarowell]

Tested virus and also bacteria with annotation. (Did not test virus with annotation though...)
Simplified the getBaseName a bit, seems to accomplish the same thing.