3.1.0 Update for LSF

What's Changed

• Feature/update install data by @buehlere in #172
• Scheduled monthly dependency update for November by @pyup-bot in #175
• Add CodeQL workflow for GitHub code scanning by @lgtm-com in #176
• Scheduled monthly dependency update for December by @pyup-bot in #177

New Contributors

• @buehlere made their first contribution in #172
• @lgtm-com made their first contribution in #176

Full Changelog: 3.0.4...3.1.0

What's Changed

• Feature/update install data by @buehlere in #172
• Scheduled monthly dependency update for November by @pyup-bot in #175
• Add CodeQL workflow for GitHub code scanning by @lgtm-com in #176
• Scheduled monthly dependency update for December by @pyup-bot in #177

New Contributors

• @buehlere made their first contribution in #172
• @lgtm-com made their first contribution in #176

Full Changelog: 3.0.4...3.1.0

Set MAX Default Read Length at 95

Modify Fastp

• setting default read 1 and read 2 max length at 95.

Remove defaults in bwa

• Remove default values for bwa -K as it causes issues in PMS2 calls.
• Also remove defaults from bwa -T as 30 is the default value

Supports Toil 5.0.1

Release supporting running Fgbio

Using Environmental Variables

Here we learned that we need:
SINGULARITY_BIND_DIR and _JAVA_OPTIONS set to use LSF successfully.