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* fix version reporting * rm unused args2 * clean modules config * pbmm2 align using prebuilt index * fix version * add samtools, switch to bgzip for downstream FAIDX compatibility * exit if qv files empty * updates to polish wf, documentation etc. * unionsum output suffix changed for compatibility with merqury * unionsum output updates * update meryl dependency of merqury * refactor create final asm * emit logs/versions, clean up * dvpolish summary * address feedback * WIP * fix redundant naming * enable phased mode dvpolish * consistent haplotype naming * remove dvpolish logic for multiple readsets/sample
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This PR:
06_polish+ deepvariant to subtool directoryAdditionally, via #343:
Clean up and standardise
POLISHsection ofmodules.configFix version reporting for some modules
Change compression tool in
CREATE_FINAL_ASMfor downstream compatibility withFAIDXFix
DVPOLISH_PBMM2_ALIGNorphan process - pass mmi index into alignmentRemoved redundant addition of
single_endmetadata field (handled inPREPARE_INPUT)Refactored
SAMTOOLS_INDEXlogic -> this indexed bams that were then merged and re-indexedPatched merqury, updated bioconda + container to fix bug causing empty scaffold qv file (meryl dependency to 1.4.1)
Edited meryl/unionsum -> merqury expects databases with
.merylsuffixRefactor
createFinalAsm.nf, include a log of changes from unpolished to polishedPublish outputs
Emit logs/versions from subworkflow
assets/notebooks/_06_assembly_polishing.qmd currently empty
Test polish subworkflow, resolve bugs
Add polish swf info to report (i.e. logic choices if contig degraded or unchanged, vs improved)
Added
DVPOLISHphased modeSwitched to merged hifi input and simplified logic to reflect this
Add tests & snapshot