update help text for fasta parameter

[kopichris]

Description of the bug

The help text for the --fasta parameter asserts that this parameter is required if --genome is not specified; however, the pipeline can function properly without specifying either parameter. Setting either parameter should only be required for genome quantification (optional) and identification of miRNAs using miRDeep2 (optional). The help text also mentions the use of a BWA index, but I believe it should be changed to a Bowtie1 index.

Command used and terminal output

Help text (fasta): This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

Relevant files

No response

System information

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