ASPEN v1.2.0

ASPEN 1.2.0

• Add hs1_chrR as a supported reference genome (T2T-CHM13 + chrR rDNA unit from Paralkar lab). (#117, @kopardev)
• Fix ZeroDivisionError in _ccbr_counts2density.py when TSS flanking bins have zero reads (e.g. genes on chrR); emit 0.0 enrichment instead of crashing. (#122, @kopardev)
• Fix object 'tdb' not found crash in ccbr_annotate_bed.R and ccbr_annotate_peaks.R for hs1/hs1_chrR genomes by adding T2T-CHM13v2.0 TxDb dispatch (pre-built SQLite shipped in nciccbr/ccbr_atacseq:v13-feat). (#123, @kopardev)
• Bump masterdocker container to nciccbr/ccbr_atacseq:v13-feat. (#123, @kopardev)
• Fix _ThreadedGzipWriter cutadapt crash in trim rule by pinning trim to nciccbr/ccbr_atacseq:v11-feat (cutadaptdocker); all other rules use v13-feat (masterdocker). (#124, @kopardev)
• Fix Error in library("org.Bt.eg.db") crash by loading bosTau9/mmul10 Bioconductor packages on-demand instead of unconditionally at script top (ccbr_annotate_bed.R, ccbr_annotate_peaks.R); org.Bt.eg.db and org.Mmu.eg.db are absent from v13-feat. (#124, @kopardev)
• Fix there is no package called 'tidyverse' crash in fixed-width peak-calling scripts by replacing library("tidyverse") with library("dplyr") in fixed_width_peakSets_to_consensus_peakSet.R, narrowPeak_normalize_pvalues.R, and narrowPeak_to_fixed_width_peakSet.R; only dplyr functions are used and tidyverse is absent from v13-feat. (#124, @kopardev)
• Fix undefined columns selected crash in ccbr_annotate_bed.R and ccbr_annotate_peaks.R when ChIPseeker cannot map T2T TxDb gene IDs through org.Hs.eg.db; ENSEMBL, SYMBOL, and GENENAME columns are now filled with NA when absent. (#123, @kopardev)
• Fix mv: cannot stat '*.annotated': No such file or directory crash in ccbr_atac_genrich_peak_calling.bash and ccbr_atac_macs2_peak_calling.bash for hs1/hs1_chrR by adding both genomes to the genome_is_known check so ChIPseeker annotation runs for T2T assemblies. (#117, @kopardev)
• Remove orphan scripts with no pipeline references: picardcloud.jar (Picard is called via in-container path /opt2/picardcloud.jar), ccbr_atac_trim_align_pe.bash (superseded by separate trim + align rules), ccbr_bam_filter_by_mapq.py, atac_assign_multimappers.py, and script1.py. (@kopardev)
• Restore ccbr_bam_filter_by_mapq.py because it is used by ccbr_bowtie2_align_pe.bash in the align workflow step. (@kopardev)
• Reduce trim rule RAM from 120 g to 48 g and increase walltime from 12 h to 16 h. (#112, @kopardev)
• Increase walltime for align, align2spikein, and atac_tss rules from 12 h to 24 h. (#114, @kopardev)
• Clarify replicateName as a biological replicate identifier in docs; add warning explaining biological vs technical replicates with lane-merging example. (#110, @kopardev)
• Document how per-sample consensus and ROI-level consensus peaks are generated, including config knobs (consensus_min_replicates, consensus_min_spm, fixed_width). (#84, @kopardev)
• Fix missing FRIP values in FRiP_stats.tsv caused by wrong cut column indices in _qc_create_frip_stats_table.bash; cut -f2,3 extracted metric labels instead of peakcaller+value — corrected to cut -f3,4. (#103, @kopardev)
• Fix DiffATAC silently skipping for all genomes except hg38 and mm10; replace hard-coded genome guard with DIFFATAC_SUPPORTED_GENOMES set covering all annotation-supported genomes (hg19, hg38, mm10, mmul10, bosTau9, hs1, hs1_chrR). (#128, @kopardev)
• Write DESeq2 size-factor-normalized counts matrix ({contrast}.normalized_counts.tsv) to the DiffATAC output directory alongside each per-contrast differential results TSV. (#68, @kopardev)
• Fix DESeq2.Rmd startup failure on systems without tidyverse by removing the unnecessary library("tidyverse") dependency; script now uses explicitly loaded packages (dplyr, ggplot2, etc.). (#128, @kopardev)