v2.1.0

[2.1.0] - 2026-08-15

Resource allocation is now declared to Nextflow rather than only passed to the tools, and there is a helper for carrying an older configuration forward.

Added

• ./PoolSeqFlow migrate_config — rebuilds parameters.config from the current template, backs the original up, carries across every setting whose parameter still exists, and reports what it kept, what is new, what the pipeline now computes for itself, and what it dropped. It refuses to carry a value the template derives, so it cannot reintroduce a stale snpEff.db or a hand-set thread count. The report is a starting point: a parameter whose behaviour changed while its value still looks ordinary will be carried across, so compare against the template afterwards.
• Every process declares cpus, so Nextflow schedules against real requirements instead of assuming one core per task. Previously three Align tasks each using ~2.2 cores ran concurrently on an 8-core machine with cpus=1 recorded for each.
• params.memory, feeding resourceLimits alongside params.threads, so one place sizes a run.

Changed

• Tools now read task.cpus rather than thread counts baked into option strings, so the number Nextflow reserves and the number the tool receives cannot diverge. Overriding cpus in a profile now changes the tool's behaviour too.
• TrimReads reserves Trim Galore's full footprint. --cores N runs N+4 threads (measured: --cores 8 peaks at 12 OS threads), so the process reserves cores.trimTotal and maps back to the worker count. A request larger than the machine now fails with Process requirement exceeds available CPUs instead of silently oversubscribing.
• JVM garbage-collection threads come from task.cpus. -XX:ParallelGCThreads was read from a config string, so cpus had no effect on SnpEff or FastQC.
• resourceLimits moved to params.threads / params.memory; it was hardcoded and would not follow a change to threads.
• Eight parameters removed after the rework left them unreferenced: the five per-tool threads values, fastqc.bundledOptions, java.garbageCollect and java.options. Each looked like a knob that did nothing.
• TrimReads no longer exports _JAVA_OPTIONS; Trim Galore 2.x is a native binary with a bundled FastQC and never starts a JVM.

Fixed

• parameters.config.template was missing parameters the pipeline requires — annotate, snpEff.runOptions, rgTagsPath, diploidy — and carried a different vcftools.minDP and different report directory names. A configuration built from it failed step 0 with RGTAGS VERIFICATION: STATUS=FAIL. The template is now generated from the reference configuration and resolves identically to it.
• Step 7 created the wrong output directory. SortRefAltByFrequency ran mkdir -p on the frequencies folder and then moved into the VCF folder, which only worked because step 6 had created it first.
• parameters.config contained the dir { } block and the reference path assignments twice, byte-identical.