v1.3 changelog

Author: CormacKinsella

CHANGELOG.md

@@ -1,127 +1,49 @@
 # Changelog
 
-### Planned
 
-- consider options for removing params from processes: done as lists within ext.args. potentially with conditional logic on metadata to provide different args.
-
-- long read support
-	- add metadata field
-	- plug in long read variant callers
-
-- deepvariant updates: now directly supports graphs
-	- also see [here](https://ucsc-ci.com/comparativegenomicstoolkit/cactus/-/blob/2dd29514027a0ad2c1a5d0ab581c7930c943fac5/doc/sa_refgraph_hackathon_2023.md#part-3-mapping-reads-to-the-graph)
-	- and [here](https://google.github.io/deepvariant/posts/2018-12-05-improved-non-human-variant-calling-using-species-specific-deepvariant-models/)
-
-- Reinstate support for topic channel version reporting in processes that use storeDir, see GH issue: https://github.com/nextflow-io/nextflow/issues/5785, currently disabled due to a Nextflow bug
-
-- Better test data with known variants of interest, add screenshots of variant calls vs genotyping outcomes
-
-- Integrate an optional input of reference assembly annotation file(s), with built in liftover to the extracted references
-
-- Support interleaved BAM input, convert to FASTQ (see EAGER)
-
-- Joint freebayes calling, or post-hoc (multiVCFanalyzer?) (see EAGER). Check also freebayes implementation in EAGER.
-
-- Check other EAGER modules
-
-- Consider mapping quality assessment: preseq, qualimap2, endorS.py (EAGER)
-
-- Consider other tools: MtNucRatio, GATK, bedtools, bamUtils, ANGSD, pileupcaller, VCF2Genome, MultiVCFAnalyzer, bcftools annotate, bcftools for genotyping/filtering, snpeff, vep, bamRefine
-	- ANGSD: instead of using pileupCaller, could use ANGSE in two separate modules: pseudo-haploid genotyping and genotype likelihoods
-
-- Consider VCF binning (e.g., HPRC deconstructs twice with different filters, also does joint calling? and then splits to sample level VCF)
-	- HPRC: -l 0 -r 10000000, then separates into SVs and small variants
-	- HPRC: -r 100000, keeping nested variants
-	- Split multi-sample VCF to single with bcftools
-	- Multiallelic sites split to bi-allelic records
-	- VCF decomposed to SNPs and indels with vcfdecompose
-	- Extract and normalise small variants with bcftools
-	- Concatenate again on sample level
-	- Similar with DeepVariant & then compare
-
-- Potential flaw:
-	- this approach assumes sample name will never be the same. But two haplotypes from the same sample will have the same sample name:
-	`vg paths --paths-file \$i --extract-fasta -x ${graph} > \$basename.fasta`
-	- add haplotype number metadata field and update metadata labelling within processes
-
-______________________________________________________________________
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-## [Unreleased]
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-## [1.3.0] - 2025-03-XX TODO: [Unreleased]
+## [1.3.0] - 2025-08-18
 
 ### Added
 
 - README.md updated with workflow output details and more information on genotyping and variant calling tools
 - Most relevant, now explicitly point out the difference between the genotyping and variant calling tools
-- TODO: detail on deepvariant and freebayes
-
-### Added
 
 - Implemented `storeDir` for outputs that need to be run once (snarls, hapl index, filter index). This is helpful when multiple users share a file system for storing graphs. Processes won't rerun even on fresh repo clones
-- These now store to a new folder next to the graph using the graph basename, e.g.: `example-unfiltered.gbz`, indexes are stored in: `example-unfiltered_indexes`
+- These now store to a new folder next to the graph based on the graph basename, e.g.: `human.gbz`, indexes are stored in: `human_indexes`
 - To ensure other stored indexes are not picked up by other stores, each index category goes into a specific subdirectory
 - Linked to adding `storeDir`, temporarily disabled topic channel version reporting from 3 modules that use it (https://github.com/nextflow-io/nextflow/issues/5785)
 
-### Added
-
 - Linear references extracted from the graph are now included as output files in `results/linear_references`
 
-### Added
-
 - ext.args template added to each module, and placeholder module config file added `conf/modules.config`
 
-### Changed
-
 - changed names of genotyping modules, channels, params etc. to increase their descriptive clarity - e.g. vg-graph-call -> vg_deconstruct, vg-map-call -> vg_genotype
 - for clarity genotyping outputs go into a genotyping folder, not variant_calling
 
-### Changed
-
 - output directory structure improved to reduce nesting, as a result of related changes to outputs
 
-### Changed
-
 - module names use consistent underscore separation, more descriptive
 
-### Changed
-
 - GAM filtering: added a param "--gamFilterMore". When false, filters only on primary alignment score + defrays ends. When true, applies MAPQ filter and discards unmapped reads
 - Under the hood this is controlled by conditional logic in `modules.config` that sets the value of `ext.args2`
 
-### Changed
-
 - Fastp previously defaulted to discard unmerged reads for aDNA samples. It now defaults to keeping them.
 - This is controlled by a parameter `--discardUnmerged` (default false)
 - Under the hood this controls FASTP `ext.args` in `modules.config`, outputting two extra fastq files for unmerged reads.
 - If these files are present, they are first concatenated with the respective merged reads before sample level concatenation and re-deduplication
 - i.e. the mapper would receiving one file per sample, containing all libraries, and both merged and unmerged reads in a single deduplicated package
 - As a result of this change, also added safety to FASTQC on receiving empty FASTQ files
 
-### Fixed
-
 - Patched non-zero exit when getting heap space for profilepmd, which would cause process to fail even if successful. Force 0 exit.
 - All output folders use underscores (no dashes) for consistency
 
+- updated DAG
 
-### Updated
-
-- TODO: updated DAG
-
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-
-
+- additional test graphs added to `data/test/additional_graphs`
 
+- added safety to FASTQC in case of empty input files (e.g. in the case of unmerged aDNA output from FASTP)
 
 
-<!-- Release history -->
 
 ## [1.2.2] - 2025-03-04