Targeting Minato

Targeting Minato v2.3.0

Major changes:

• Flash and Trimmomatic are replaced with Fastp by @trevormartinj7, @Snicker7, and @Colelyman
• Guardrails (checking experimental conditions and raising warnings) by @Snicker7
• Failed runs are displayed with the error by @trevormartinj7

Minor changes:

• Replace link to CRISPResso schematic with raw URL in README by @Colelyman in #329
• Fix samtools piping by @Colelyman in #325
• Prime editing alignment params by @kclem in #336
• Fix for recent Matplotlib v3.8 by @mbowcut2 in #346
• Enable quantification by sgRNA by @kclem in #348
• Fix Matplotlib breaking change issue by @mbowcut2 in #352
• Fix assigning multiple qwc by @Snicker7 in #375
• Run unit tests via Github Actions and fix matplotlib character issue by @Snicker7 and @mbowcut2 in #386
• Remove future Pandas warnings and sort CRISPRessoCompare tables by @mbowcut2 and @Snicker7 in #389
• Fix interleaved fastq input in CRISPRessoPooled and suppress CRISPRessoWGS params by @Colelyman in #392
• Fix #367, reads only align to prime edited amplicon, not to reference by @mbowcut2 in #393
• Run integration tests on every push by @Snicker7 in #394
• Move read filtering to after merging in CRISPResso by @Colelyman in #397
• Fix the assignment of multiple quantification window coordinates by @Snicker7 in #403
• Decrease Docker image size and fix PE naming and parameter behavior by @Colelyman, @Snicker7 and @mbowcut2 in #404
• fix space character in README by @DennyDai in #400
• Fix Jinja2 undefined variables by @Colelyman in #417
  Full Changelog: v2.2.14...v2.3.0