alpha.6 #274
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alpha.6 #274
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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
Add documentation
* 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
* 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 <bwingfield@ebi.ac.uk>
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May 23, 2024
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