ASPEN 1.1.2

• Fix broken data path for biowulf. (#104, @kelly-sovacool)
• Remove deprecated ccr partition. (#106, @kelly-sovacool)

ASPEN 1.1.1

• Fix Diffatac error (#101, @kopardev)
  • Adds a defensive check to prevent invalid 'row.names' length error when up_roi or down_roi are empty (due to strict FC/FDR thresholds in DiffATAC)
• Minor refactoring to accomodate moving to ccbr_tools >= v0.4 (#101, @kopardev)

ASPEN 1.1.0

This version features a major overhaul of the pipeline with changes in the following areas:

Spike-in alignment (#94, @kopardev)

• Added support for spike-in alignment and scaling factor computation. (#94, @kopardev)
• This new feature is controlled by two new parameters in the config file: spikein and spikein_genome. (#69)

Peak-calling (#94, @kopardev)

• Peak-called narrowPeak files are now q-value filtered by default, with a default q-value threshold of 0.1. Unfiltered files are still available for users who want to apply their own filters. (#90)
• Streamlined the output directory structure.
• Added the name of the peak-caller to ROI filenames (#86)
• Added missing annotations (#79)

Differential accessibility (#94, @kopardev)

• Add new rules for scaling counts and annotating regions of interest. (#68)
• DiffATAC analysis is now run for both MACS2 and Genrich peak calls, with results stored in separate directories.
• DiffATAC analysis now includes spike-in scaling factors when spikein is TRUE.
• Removed redundant steps in the differential accessibility analysis to streamline the process.
• create Tn5-based and reads-based counts matrices (#67)
• create spike-in scaled counts matrices (#62)
• Quality control
  • Updated FRiP calculation to use tagAlign.gz files instead of deduplicated BAM files.
  • Removed unnecessary QC metrics and simplified the QC workflow.
  • Updated TSS enrichment and fragment length distribution rules to align with the simplified pipeline structure.

Output directory (#94, @kopardev)

• Consolidated peak calling outputs into a single directory for each peak caller. (#91)
• Simplified the output directory structure. (#92)
• Decreased output digital footprint by removing unwanted intermediate files, gzipping annotated files, etc. (#87)
• Improved slurm job logging with jobby (now depends on ccbr_tools v0.4). (#98, @kelly-sovacool)

Documentation (#94, @kopardev)

• Simplified the documentation to focus on the core functionalities of the pipeline, as well as reflect all of the changes in this version.

v1.0.6

ASPEN 1.0.6

• fix: dockername typo (#57, @kopardev)
• docs: update documentation, change theme (#77, #78, @kopardev)

ASPEN 1.0.5

• fix: ucsc tool version changed requiring newer version of GLIBC (#54, @kopardev)
• using new masterdocker v11

ASPEN 1.0.4

• fix: DiffATAC failure (#46, @kopardev)
• fix: last line of contrasts.tsv read in correctly; black lines ignored (#48, @kopardev)
• fix: ROI calculation from fixed-width consensus peaks no longer tried to fix the peak width again (#50, @kopardev)
• feature: create diffatac results from MACS2 peaks (#51, @kopardev)
• fix: BUYINPARTITIONS fixed in wrapper for BIOWULF-only (#52, @kopardev)

ASPEN 1.0.3

• fix: No module named 'numpy._core._multiarray_umath' error withunset PYTHONPATH (#43, @kopardev)
• fix: jobby command points to the correct location of snakemake.log file
• ASPEN is now archived on Zenodo, you can cite it with the DOI 10.5281/zenodo.13755867. (#42, @kelly-sovacool)

ASPEN 1.0.2

• Set the singularity cache dir if --singcache is not provided. (#37, @kelly-sovacool)
• ASPEN now has a documentation website: https://ccbr.github.io/ASPEN

v1.0.1

• documentation updated
• differential ATAC working

v0.6.1

• correction to fqscreen cattle path

v0.6

• support for mmul10 (Macaca) and bosTau9 (cattle) genomes
  • created resource files: indexes, promoter files, tss files etc.
• Added Macaca and Cattle to fastqscreen indexes
• support increased from 4 replicate to 6 replicates
• macs and genrich fixed width peaks generation rule added
• docker updated to v10 (genome support and tidyverse added)

v0.5.3

Includes reference files for mmul10

v0.5.2

• atac_assign_multimappers.py now getting query sorted input
• dryrun log saved in workdir
• local (workdir) scriptsdir used