Improve pca #267
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Improve pca #267
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… memory footprint very low (but higher I/O into tempfiles)
nebfield
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May 24, 2024
* Check for _ in sampleset names * fix samplesheet path to point to VCF * drop vcf suffix * update tests with removed vcf suffix * include inputs when relabelling (geno and sample files are unchanged) * add more tests for results structure * Expose documentation about switching versions. * add cloud / JSON samplesheet docs * add multiple chromosomes example * add links to JSON samplesheet * explicitly set default results to $PWD/results this change affects people running the workflow directly from github, e.g. $ nextflow run pgscatalog/pgsc_calc ... if --outdir isn't set, then the results folder can be in $NXF_HOME, which is a hidden folder in the home directory by default. not a helpful place for results to be! this doesn't affect people running from a cloned repo directly * Fix typo in output.rst * Add in documentation about popsimilarity file. * migrate to pygscatalog utilities (#296) * add correlation test * add correlation action * fix download URL * use scoring files from correlation archive * get test profile working with pygscatalog * integration updates * fix correlation scorefile wildcard * fix tests * update plink2 * gzip afreq in plink2_vcf * update custom scoring files for liftover * fix match module test * use local files in test suite * fix singularity container definition * check for environment variables with set -euxo * logs are massive, don't upload, debug locally * Improve pca (#267) * Output allele frequencies along with missingness (for filtering variants) * Add afreq to output * Add afreq to intersect_variants.nf * add afreq to intersect_thinned * intersect with new pgscatalog-intersect application * rebase * Make verbose * Remove duplication * Use new output of intersect_variants in filtering * Use new output of intersect_variants in intersect_variants.nf : keeps memory footprint very low (but higher I/O into tempfiles) * Fix column index to PCA_ELIGIBLE (13) * Fix awk statement that doesn't work with odd carriage return? * Fix awk statement for True/False (not 0/1 as in previous version) * Add in variant-based filters --------- Co-authored-by: Benjamin Wingfield <[email protected]> * remove duplicate container definition (pygscatalog) * fix duplicate freq flags * bump workflow version * don't upload output directory in ancestry tests * add docker uid runOption to test config * just use working directory as tmpdir * drop deprecated docker.userEmulation * update upload-artifact to v4 * fix join failure caused by wrong meta in afreq output (VCF) * Superseded by pgscatalog-intersect * Update pgscatalog_utils conda environment * use stable container tags * bump pgscatalog.core version --------- Co-authored-by: Benjamin Wingfield <[email protected]>
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Will use new python-based intersect variants to implement MAF/missingness filters to define variants in the target dataset that are PCA-eligible: https://github.com/PGScatalog/pygscatalog/blob/match_intersect/pgscatalog.match/src/pgscatalog/match/cli/intersect_cli.py