* chore: version tag * chore: set the current singularity cache dir * refact: changes to config required for #45 * refact: scale down comput requirements for shorter queues * feat: adding chrom sizes as resources * feat: updates to peakcalling; default peaks will be filtered by q-value; unfiltered peaks will still be saved separately * feat: change bowtie2 alignment commands to save intermediate files correctly * feat: tn5nicks.bam are separated by peak caller * refact: mostly changes suggested by pre-commit * refact: FRIP is calculated from dedupBAM for each peak caller * feat: adding new python scrip to convert bams to tn5beds * feat: new script required by spike-in scaling * chore: add aspen.bak to gitignore * feat: updates to rules to incorporate spike-in normalization; revamp peak calling itself * feat: adding test wrapper script * feat: adding docs figures * feat: adding flowchart * feat: major updates to documentations * refact: fix #92 * refact: fix #85 * refact: fix #91 * feat: add +pymdown-extensions to requirements * feat: fix $91 * feat: fix #87 * refactor: pre-commit fixed * fix: operating system and the processor support error in bwa * fix: argument is -n and not -b * fix: OUTNPS can be a comma separated list * fix: operating system and the processor support Intel error * fix: avoid moving the consensus file to itself * fix: annotate_roi produced .gz annotated file * refactor: annotated files are now .gz * fix: bash variable have single curly-brackets inside bash script * refactor: annotated files are now .gz * fix: consensus_annotated is output not params * fix: annotated is now gz * refactor: update output file naming conventions for peak calling rules and remove unused spikein rule smk * docs: add detailed peak annotation folder and update output descriptions * chore: update CHANGELOG.md for ASPEN 1.1.0 release with general, configuration, alignment, peak calling, differential accessibility, quality control, documentation, script, output structure, and miscellaneous changes * docs: update CHANGELOG.md to include recent changes in alignment, peak calling, differential accessibility, and output structure * refactor: improve argument validation and usage instructions in run_tests.sh * chore: Update CHANGELOG.md * chore: remove version from docs * chore: reformat CHANGELOG.md --------- Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

reorg the peaks folder #92

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