Drop aggregation during report generation #249
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smlmbrt
reviewed
Feb 22, 2024
re-sync nf-core
Docs to explain cache
Remove storeDir semantic structure
nebfield
added a commit
that referenced
this pull request
Mar 19, 2024
* Update base.config Match error-handling from nf-core (solves problem with status 140 that I had) * Use groovy to parse samplesheets (#243) * implement groovy functions for samplesheet parsing * set up utility class * add build to map * add json support * rename json parser * delete samplesheet module * remove mount docs (deprecated) * remove out.json from expected test output * fix parsing vcf samplesheet * Update report (renv and include licenses) (#203) * fix report link and setup renv lockfile * update dockerfile to use renv * add license terms * clarify custom scores + licenses * keep empty file in assets folder for optional input * Drop aggregation during report generation (#249) * drop small sampleset warning when integrating reference data * drop aggregation * update lockfile: drop data.table * load scores the same way * bump utils version * drop effect_type (shouldn't actually be in columns array) * use dev image * update score test * fix test * bump pgscatalog_utils version * boring but big: re-sync nf-core * fix cache error in report * nf-core resync * set deno dir * update schema * set up auto-generated environment * set workDir consistently * improve caching * fix help * set outdir default * use binary packages to build report image * fix missing dependencies * fix fraposa_pca * add storeDir to relabel_ids * fix score metadata in report * store results permanently * write to genotypes_cache, if set * update conda * add custom example scorefile * Update schema to say what the cache is for * Add information on cache and pipeline speed * Not only for -resume * fix storeDir * fix tempdir on HPC/singularity * gcp compatbility updates * remove semantic structure from storeDirs (bad) * Update cache.rst * don't copy twice * bump report singularity version * fix quarto * fix output * fix fraposa * fix capturing intersect counts --------- Co-authored-by: smlmbrt <sam.a.lambert@gmail.com> * Fix cache names (#260) * Update plink2_makebed.nf Remove chromosome so that it doesn't cause cache collision (should only run once per sampleset anyways) * Fix prefix and output names * Remove chromosome ID from orient * set pytest version * fix node deprecation warnings * bump pytest-workflow * downgrade pytest * fix node deprecation warning * bump python action again * fix tmpdir errors in report * fix --genotypes_cache * make temporary dir in working directory * fix missing cachedir * cache relabelled afreq and variants separately * oops * add changelog to docs * bump report from dev to production * fix report distribution plots for non-ancestry runs * Update arm.rst with new profile * add deeep cache * stop using wildcards * swap cross operator -> combine * set pgscatlaog_utils version to v0.5.2 * fix log output * fix match_combine cache * oops * fix score aggregation cache * error if scoring files don't get a calculation result * update error strategy * fix missing quarto package * Fix race condition in cache (#262) * stop using global variables * use local variables * Add information about versions * add version to report (#265) * add version to report * update author --------- Co-authored-by: Sam Lambert <sam.a.lambert@gmail.com>
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Also, stop warning about small sample sizes with
--run_ancestry(allelic frequencies are loaded from reference panel)