Changelog¶

v1.0.9 — 2026-05-13¶

SLURM partition compatibility. Added --slurm_queue parameter (required with -profile slurm) to specify the target SLURM partition. The pipeline now exits immediately with a clear error message if this parameter is missing when running on SLURM. The partition should allow a maximum walltime of at least 7 days; shorter limits (1–2 days) may work for small genomes or low-depth sequencing.

BAM files are now deleted mid-run after all GATKHC tasks complete.
A new cleanupBAMs process receives a count-based sentinel that resolves only after every GATKHC task across all intervals has emitted. This guarantees that no BAM is removed while any interval job still needs it, yet reclaims the space as soon as the last GATKHC finishes — without waiting for the full pipeline to succeed. BAMs from --bam_input runs are never touched.
Fixed zero-length vector crash in r_process_summary_fastp.R for SE samples.
as.numeric(NULL) produces a zero-length vector, which silently corrupted the summary matrix. Both duplication$rate and insert_size$peak now use an explicit length(v) == 0 guard before assignment.

Replaced CombineGVCFs with GenomicsDBImport for GVCF consolidation.
The legacy CombineGVCFs step has been replaced by GATK's GenomicsDBImport, which uses on-disk TileDB storage instead of in-memory merging. This eliminates GC-thrashing at large sample counts (tested at 1,605 samples). Batch size is configurable via --genomicsdb_batch_size (default: 50, the Broad production default).

log.info banner moved inside the workflow block — top-level executable statements are no longer permitted in Nextflow 26.x.
C-style for (int i = ...) and while loops replaced with Groovy functional expressions (takeWhile/collect, .step().each).
${HOME} environment variable interpolation in nextflow.config replaced with env('HOME') — bare env-var interpolation was removed in Nextflow 26.x.

JVM flags -XX:-UsePerfData --enable-native-access=ALL-UNNAMED added to all GATK processes to suppress Java 17+ module-restriction warnings and /tmp/hsperfdata_* lock conflicts under concurrent Singularity jobs.
gatkIndex base memory increased from 2 GB to 4 GB to prevent a -Xmx0g crash on the first attempt.
Fixed r_process_summary_fastp.R crash on single-end samples: j$insert_size$peak is NULL for SE data; as.numeric(NULL) produces a zero-length vector that silently failed the matrix assignment. Now handled with an explicit length check.

Automatic Singularity image download.
All container images are pulled automatically by Nextflow on the first run — no manual singularity pull step is needed. Images are fetched from quay.io/biocontainers and cached in $HOME/.singularity/cache (configurable via singularity.cacheDir). Subsequent runs reuse the cached images without re-downloading.
Bundled example dataset.
The repository ships with a ready-to-run E. coli LTEE example (example/) that lets you verify your setup end-to-end. Three public SRA samples (SRR2589044, SRR2584863, SRR2584866) mapped against the REL606 reference genome serve as the test case. See Getting started → Step 4 for instructions.

Switched all R processes to rocker/tidyverse:4.4.3 for a reliable, actively maintained R environment.
Improved QC HTML report: accessible Okabe-Ito colour palette, version and runtime metadata in the header, auto-zoomed BWA mapping-rate axis, violin + jitter distribution plot.
Fastp JSON summary parsing rewritten with jsonlite to correctly separate before- and after-filtering statistics.
Fixed geom_vline(linewidth=) for ggplot2 ≥ 3.5 compatibility.
Singularity autoMounts enabled and environment whitelist added for seamless APPTAINER/SINGULARITY work-directory binding on HPC.
Pipeline statistics report (pipeline_statistics.nf) consolidated from per-process output files.

See the GitHub commit history for changes prior to v1.0.6.