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
andspikein_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
isTRUE
. - 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.
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 with
unset 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
ASPEN 1.0.1¶
- differential ATAC updated
- documentation updated
ASPEN 1.0.0¶
- completely dockerized
- differential ATAC
ASPEN 0.6.1¶
- correction to fqscreen cattle path
ASPEN 0.6¶
- 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)
ASPEN 0.5.3¶
- Includes reference files for mmul10
ASPEN 0.5.2¶
- atac_assign_multimappers.py now getting query sorted input
- dryrun log saved in workdir
- local (workdir) scriptsdir used
ASPEN 0.5.1¶
- typo fix in main wrapper script
ASPEN 0.5¶
- fastqscreen added
- minor bug fixes
ASPEN 0.4.1¶
- Bug fixes
- minor updates
ASPEN 0.4¶
- Multiqc edits
- README updates
ASPEN 0.3¶
- FRiP calculations added
ASPEN 0.2¶
- Peak motif enrichment with homer/meme
- Peak replicate/sample/peakcaller PCA comparisons after bedtools jaccard pairwise calculations
ASPEN 0.1¶
- first working version
- calls peaks with macs2/genrich
- annotates peaks with chipseeker (human and mouse support)