Version 0.6.0 updates #58
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…rdised but users can change the scaling directly in the rule
…pdate documentation
…d connect to pipeline
…mlRho to be compatible in a given pipeline run
…_vcfs.smk and to describe the file content better
…BCF file can either be filtered for sex chromosomes (autos) or not (genome)
…iles or with autosomal-only BCF files
…mappings because the *bai files are temporary files and because it is unnecessary
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Oct 6, 2023
…merge_vcfs.smk so that these rules are run only once if both steps are run
…ded or for the whole genome if not
…or modern samples only
Optional removal of sex chromosomes from VCF files
…tween setting up singularity and conda and running GenErode
…ointed to RepeatMasker libraries
… be required in the new container
… by the latest repeatmodeler version
Update repeatmodeler to version 2.0.4 to handle large genomes
… merging when testing different filtering levels for missingness
…gering reruns of downstream rules
…ered VCF file when the pipeline is only run for modern or historical samples, respectively, avoiding generation and storage of duplicate VCF files
…t extraction of historical or modern samples is avoided when running the pipeline for only historical or only modern samples
…only run for one dataset
…this file is not required
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A test run of the repeat identification step with a large reference genome finished successfully |
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