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…flanking bins are zero When all 20 flanking TSS bins have zero reads (e.g. genes on chrR with no ATAC background), flankavg=0 caused a ZeroDivisionError. Now emits 0.0 for all density values and reports TSS enrichment as 0.0 rather than crashing. Closes #122 ⚡ generated using AI ⚡
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Applied fix for issue #122 in commit 19dcbf5: Bug fixed: Change: Added a zero-guard after computing Issue #123 (missing |
5 tasks
…iner to v13-feat - Add hs1/hs1_chrR branch to ccbr_annotate_bed.R and ccbr_annotate_peaks.R genome dispatch chains; loads pre-built T2T-CHM13v2.0 TxDb from /opt2/annotation/TxDb.Hsapiens.NCBI.T2T.CHM13v2.0.sqlite via AnnotationDbi::loadDb(); adb remains org.Hs.eg.db - Bump masterdocker from nciccbr/ccbr_atacseq:v11-feat to v13-feat (ships the pre-built TxDb sqlite; no seqlevelsStyle<- needed) - Update --genome help strings in both scripts - Update CHANGELOG Closes #123 ⚡ generated using AI ⚡
…pWriter bug The monolithic ccbr_atacseq:v13-feat container ships a cutadapt version that triggers 'AttributeError: _ThreadedGzipWriter object has no attribute name' when running with -j >1 on gzip output. Pin the trim rule to the dedicated nciccbr/ccbr_cutadapt_1.18:v3 container (cutadaptdocker), which ships cutadapt 1.18 — predates the _ThreadedGzipWriter class entirely. - Add cutadaptdocker key to config/config.yaml - Change trim rule container from masterdocker to cutadaptdocker - Update CHANGELOG ⚡ generated using AI ⚡
… cutadapt bug in v13-feat ccbr_cutadapt_1.18:v3 lacks /opt2/TruSeq_and_nextera_adapters.consolidated.fa. Use v11-feat for the trim rule instead — has working cutadapt and the required adapter FASTA. v13-feat remains masterdocker for all other rules (annotation TxDb support). ⚡ generated using AI ⚡
org.Bt.eg.db, org.Mmu.eg.db, TxDb.Btaurus.UCSC.bosTau9.refGene, and TxDb.Mmulatta.UCSC.rheMac10.refGene were unconditionally loaded at the top of ccbr_annotate_bed.R and ccbr_annotate_peaks.R. The v13-feat container is missing org.Bt.eg.db, causing an immediate crash for all genomes (including hs1_chrR) even though those packages are never needed. Move TxDb loads into their respective dispatch blocks; OrgDb packages (org.Bt.eg.db, org.Mmu.eg.db) are dropped from explicit library() calls entirely — ChIPseeker loads them dynamically via annoDb=. ⚡ generated using AI ⚡
…cripts tidyverse is absent from nciccbr/ccbr_atacseq:v13-feat. The three affected scripts (fixed_width_peakSets_to_consensus_peakSet.R, narrowPeak_normalize_pvalues.R, narrowPeak_to_fixed_width_peakSet.R) only use arrange/mutate/filter, all of which are in dplyr — already installed. ⚡ generated using AI ⚡
When ChIPseeker's annotatePeak cannot map TxDb gene IDs through org.*.db (e.g. T2T/hs1_chrR assemblies using a RefSeq-based SQLite TxDb), the ENSEMBL, SYMBOL, and GENENAME columns are not added to the result data frame. The subsequent column selection then crashes with 'undefined columns selected'. Fill the missing columns with NA_character_ before the merge so annotation still succeeds and emits NA for those fields. ⚡ generated using AI ⚡
The genome_is_known check in ccbr_atac_genrich_peak_calling.bash and ccbr_atac_macs2_peak_calling.bash only recognised hg19/hg38/mm10, so RUNCHIPSEEKER was forced to False for hs1/hs1_chrR. This caused the per-replicate .annotated files never to be created, then the unconditional mv in the FILTERPEAKS loop failed with 'No such file or directory'. Both hs1 and hs1_chrR are now supported: nciccbr/ccbr_atacseq:v13-feat ships a T2T CHM13v2 SQLite TxDb and the R annotation scripts have been updated to dispatch to it. ⚡ generated using AI ⚡
Document the four fixes from this session that were committed but not yet logged: - org.Bt.eg.db on-demand loading (#124) - tidyverse → dplyr in peak-width R scripts (#124) - NA fallback for ENSEMBL/SYMBOL/GENENAME in annotation scripts (#123) - hs1/hs1_chrR genome_is_known in peakcalling bash scripts (#117) ⚡ generated using AI ⚡
The following scripts are unused by any pipeline rule or helper script: - picardcloud.jar: Picard is called as /opt2/picardcloud.jar inside the container; the local copy is never mounted or referenced. - ccbr_atac_trim_align_pe.bash: superseded by separate trim + align rules. - ccbr_bam_filter_by_mapq.py: no references anywhere in the codebase. - atac_assign_multimappers.py: mentioned only in a comment in align.smk, never executed. - script1.py: no references anywhere in the codebase. ⚡ generated using AI ⚡
⚡ generated using AI ⚡
The pieplot chunk in DESeq2.Rmd only built roiAnnodf for hg38/mm10, so the diffatac rule crashed with "object 'roiAnnodf' not found" for every peakcaller/method/contrast combination when genome is hs1 or hs1_chrR. Add a matching branch that loads the T2T CHM13v2.0 TxDb, mirroring the pattern already used in ccbr_annotate_bed.R/ ccbr_annotate_peaks.R (#123), and backfill ENSEMBL/SYMBOL/GENENAME with NA when ChIPseeker can't map T2T gene IDs, since SYMBOL is referenced later in the volcano plot chunk. Fixes #125 _commit message is ai-generated_
…nge values
create_tn5bams failed at bedToBam with "Start Coordinate detected that
is < 0" for reads near chromosome boundaries, because Tn5 cutsite and
read-end shifts (+4/-5) were applied without bounds checking.
- ccbr_atac_bam2tn5bed.py: add parse_genome_sizes()/clamp_interval()/
tn5_cutsite() helpers; require --genomefile to clamp every tn5 and
read interval into [0, chrom_len]; skip unmapped/secondary/
supplementary pairs and unknown chromosomes; emit per-read Tn5
cutsite entries; report pairs_seen/written/skipped and
clipped/skipped counters to stderr for QC.
- align.smk: pass --genomefile {params.genomefile} (already defined
for the existing bedToBam calls) through to the script.
Fixes #124
_commit message is ai-generated_
… support The diffatac/diffatac_aggregate rules ran in the baser container (nciccbr/ccbr_baser:230531), which has all R packages DESeq2.Rmd needs but lacks the T2T-CHM13v2.0 TxDb sqlite baked into masterdocker (nciccbr/ccbr_atacseq:v13-feat). This caused hs1_chrR diffatac runs to fail with "DB file '/opt2/annotation/TxDb.Hsapiens.NCBI.T2T.CHM13v2.0.sqlite' not found" after the roiAnnodf fix in #125 started working. masterdocker has been rebuilt with the previously-missing packages (tidyverse, DT, pander, ggfortify, EnhancedVolcano, ComplexHeatmap; see CCBR/Dockers2#426), so diffatac/diffatac_aggregate now use masterdocker instead, and the now-unused baser container entry is removed from config.yaml. Also drop two other container entries (fastqcdocker, ucscdocker) confirmed unused by any rule. Fixes #126 _commit message is ai-generated_
Use the latest ccbr_tools symlink (currently v0.7) instead of pinning to v0.4, so the pipeline picks up ccbr_tools updates without requiring a config change each time. _commit message is ai-generated_
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Changes
Add
hs1_chrRas a new supported genome in ASPEN — the T2T-CHM13 assembly with the rDNA repeat unit (chrR) appended.hs1_chrR.blacklist.fa.gz,hs1.promoters.bed.gz, frip beds, and tssBed tarballs via Git LFS.gitattributesLFS tracking entries for the new resource fileshs1_chrRgenome stanza toconfig/config.yamlwith user-facing commenths1_chrRtoSUPPORTED_GENOMESin theaspenCLI wrapperhs1_chrRindocs/deployment.mdanddocs/limitations.md(with rDNA scientific rationale tip box)resources/chroms/hs1_chrR.chromslisting chr1–chr22, chrX, chrY, chrRCHANGELOG.mdentryIssues
Closes #117
PR Checklist
CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/