v2.0.0-alpha.5 #244
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v2.0.0-alpha.5 #244
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Match error-handling from nf-core (solves problem with status 140 that I had)
* 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
* fix report link and setup renv lockfile * update dockerfile to use renv * add license terms * clarify custom scores + licenses
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Feb 26, 2024
* 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>
* 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
* stop using global variables * use local variables
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Mar 19, 2024
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smlmbrt
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Mar 19, 2024
* add version to report * update author
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closes #240 #207 #134 #209 #111 #245