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v2.1.1

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@ozankiratli ozankiratli released this 15 Aug 21:59
· 180 commits to main since this release
v2.1.1
3fd831b

[2.1.1] - 2026-08-15

A stability release. Nothing new to configure and no change to how a run is invoked — this closes the gaps where a result could be quietly wrong or quietly irreproducible. An existing parameters.config needs no changes.

Added

  • Step 0 refuses to run when the analysis parameters changed since the existing outputs were produced. Completed steps are skipped by looking for output files, not by checking what produced them, so a changed poolSize or filter threshold would otherwise leave one output folder holding results from two different settings. The values behind a set of outputs are recorded in .poolseqflow_params and mirrored to a read-only Output/run_parameters.txt. Path, resource and software parameters are excluded; anything added in a later release counts as analysis-affecting until decided otherwise.
  • Step 0 refuses to run when RGTags.csv changed after the file was consumed. The tags are written into the BAMs at step 4 and the row order is fixed into the VCF at step 6, and neither is re-derived once its output exists. The report separates a changed tag value (invalidates Ready/, VCF/, Frequencies/) from a reordering (invalidates VCF/, Frequencies/ only) and names the folders to delete; deleting them is what clears the check. Projects whose outputs predate this release adopt their current file as the baseline, with a note to confirm it against the BAM headers.
  • Sample columns follow RGTags.csv row order, so results come out arranged the way the samples were laid out rather than however they sort as strings. Where several rows share an SM, the merged column takes the position of the first of them.
  • Duplicate ID detection. A row is looked up by ID and only the first match is read, so a repeated ID silently discarded the later rows and gave that sample the wrong tags — producing a perfectly valid BAM that nothing downstream could flag.
  • CRLF repair for RGTags.csv. A file saved from Excel on Windows carries a stray carriage return into the last tag of every row; it previously failed with Invalid tag 'PU', which names nothing useful. Step 0 now rewrites the file with Unix line endings, preserving permissions and ownership, and reports RGTAGS LINE ENDING CHECK: FIXED.
  • bin/atomic_mv.sh — moves that cross a filesystem boundary now stage through a .part file and rename into place.

Changed

  • workDir is now under mainDir. It was a relative path, so the scratch/permanent split the pipeline documents was not actually in effect — work directories landed wherever the pipeline was launched from.
  • Variant calling receives its BAMs in a defined order. collect() emitted them in task-completion order, so the sample column order of the VCF varied between runs on identical input; three consecutive runs gave three different orders. The sort keys on the sample id, because the file paths begin with Nextflow's work-directory hash and sorting those is no better than chance.
  • All 22 cross-filesystem moves are atomic. A plain mv across filesystems is a copy followed by an unlink, so a job killed mid-move left a truncated file under its final name — which the existence-based skip logic then accepted as a completed step.
  • reset is behind a typed DELETE_MY_ANALYSIS confirmation and also clears .poolseqflow_params and .poolseqflow_rgtags, which would otherwise fail the next run's checks against outputs that no longer exist.
  • clean and reset resolve paths through nextflow config rather than parsing parameters.config as text. Values are interpolated, so text matching returned the wrong path.
  • RGTags.csv.template now shows the replicate and SM-merge pattern, with DS carrying a per-replicate descriptor instead of repeating the sample name.

Fixed

  • The sensitivity formula in bin/filterFalsePositives.sh -h was missing a factor of two. It read s = 1 / ([DIPLOIDY] / [POOLSIZE per SAMPLE]) and should read s = 1 / 2 * ([DIPLOIDY] / [POOLSIZE per SAMPLE]). Help text only — anyone who ran the script by hand and followed it would have passed the wrong -s.

Commits

  • Minor fix in help for manual use (6e18762)
  • Parameter change detection added. (715f822)
  • workDir and reset fixes (f73b33d)
  • Output parameters to a file (0f5666f)
  • File move process improved (408efb4)
  • Sample ordering in vcf fixed. NF orders samples first come first serve (dc2ea72)
  • Sample ordering in vcf fixed. RGTags guardrails added. (4a9f89d)
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