Handle new reference naming #173
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…GRCh3#_*.king.cutoff.out.id") with a single meta ID. ToDo: rename the deg2 relatedness files in setup_resource.nf / bootstrap_ancestry.nf
smlmbrt
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Oct 2, 2023
nebfield
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Oct 2, 2023
nebfield
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Oct 3, 2023
* Allow VCF inputs with variable chromosome fields, but filter the variants to canonical or user-specified chromosomes. * Fix test * Documentation edits for VCF import * typo * Clairification on sampleset naming conventions (also enforced in check_samplesheet within utils) * set up offline testing * fix singularity url * update samplesheets * fail when join goes bad * make meta key for vmiss match converted vcf * fix --only_projection * add vcf ancestry test * fix plink call * what's wrong with my yaml :( * arf * double arf * I hate yaml * fix test name * activate ancestry vcf singularity test * fix test name * add retry for score and combine (often runs out of RAM on larger datasets) * Bump utils to v0.4.2 (#185) * bump v0.4.1 -> v0.4.2 * remove whitespace * fix tag * Fix conda action on publish (#184) * fix finding mamba * test ancestry with conda too * fix mamba profile * remove matrix from ancestry * fix conda channel message * Fix plink2_score options (#181) * Add mean-imputation back to scoring when samples aren't using a reference panel * Ignore allele frequency calculation ONLY when we have a reference, else just calculate allele frequencies on scoring file variants (with --extract) * Only use --error-on-freq-calc when non-mean-imputation is applied. Use extract to consider only variants from the scoring file. * Better comment placement * update test to match behaviour * fix test * add token to avoid rate limit * check plink log more thoroughly --------- Co-authored-by: Benjamin Wingfield <[email protected]> * Note about score precision (Closes #162) * Handle new reference naming (#173) * More default memory for plink, needed for a bigger reference (gnomAD). * More generalized file pattern for relatedness files in a reference ("GRCh3#_*.king.cutoff.out.id") with a single meta ID. ToDo: rename the deg2 relatedness files in setup_resource.nf / bootstrap_ancestry.nf * Update report.qmd to handle other colours * give king cutoff files consistent names * fix test * add version check to extract_database * add version check to extract_database --------- Co-authored-by: Benjamin Wingfield <[email protected]> * Update changelog.rst * Version reference database with parameter (#189) * version reference db separately * Update RELEASE-CHECKLIST.md Information about the ancestry version --------- Co-authored-by: Sam Lambert <[email protected]> --------- Co-authored-by: smlmbrt <[email protected]>
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ToDo:
GRCh3#_{meta.id}.king.cutoff.out.id, examples: GRCh37_gnomAD.king.cutoff.out.id, GRCh38_gnomAD.king.cutoff.out.id