Adding WILDS WDL modules for bowtie & bowtie2

[tefirman]

Type of Change

• New modules

Description

Adds two new alignment modules to the WILDS WDL library:

• ww-bowtie - Short-read alignment using Bowtie (v1.3.1), an ultrafast, memory-efficient aligner optimized for reads up to ~50 bp. Includes bowtie_build and bowtie_align tasks.
• ww-bowtie2 - Sequence alignment using Bowtie 2 (v2.5.4), a fast and sensitive gapped-read aligner supporting variable-length reads. Includes bowtie2_build and bowtie2_align tasks.

Both modules support paired-end and single-end alignment, produce sorted BAM + BAI output via samtools, and follow existing WILDS conventions (matching the ww-bwa module pattern).

Testing

How did you test these changes?
Ran testrun.wdl for both modules using test data from ww-testdata (reference genome + FASTQ files). Both paired-end and single-end samples aligned successfully.

What workflow engine did you use?
Sprocket (v0.18.0)

Did the tests pass?
Yes - both modules produce sorted BAM and BAI files for all test samples. Sprocket lint also passes clean.

Documentation

• I updated the README (if applicable)
• I added/updated parameter descriptions in the WDL (if applicable)
• I ran make docs-preview to check documentation rendering (if applicable)

Additional Context

Both Docker images (getwilds/bowtie:1.3.1 and getwilds/bowtie2:2.5.4) were updated to include samtools for BAM conversion/sorting within the alignment tasks.

[emjbishop]

Some minor suggestions