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* adding viloca to the workflow * fix file paths * update conig_schema * adding paired_end_read_merger * update rule for paired_en_read_merger + add conda env definition * update rule for paired_en_read_merger + add conda env definition * update enviroment * add paired_end_read_merger * update paired_end_read_merger rule * add conda package to env * Viloca touch ups - snakemake handles `directory()` - VILOCA 1.0.0 on bioconda - use GitLab for smallgenomeutilites due to GitHub LFS limitations * Linting * Generate copnfig manual * Documentation touch ups - update paper: V-pipe 3.0 pre-print - WorkflowHub's required documentation.md points to our documentation - Update Tutorial intro page: point to installer * improve tutorial_0_install.md * Links to bioconda in installation tutorial * Singularity+conda support * Update README.md with viloca reference * Add issue templates * Contributing guidelines * Disable linter for templates * bugfix: viloca - typo fix - all: depends on correct CSV * bugfix: bump versions of bcftools and cyvcf2 - recent change of numpy in bioconda breaks older cyvcf * [bump] LolliPop 0.4.0 - support new `filters` option * Update of conf manual * [bump] LolliPop v0.4.1 --------- Co-authored-by: Ivan Blagoev Topolsky <ivan.topolsky@bsse.ethz.ch> Co-authored-by: Prajwal Kulkarni <prajwalkulkarni76@gmail.com> Co-authored-by: Ivan Blagoev Topolsky <ivan.topolsky@sib.swiss>
…not run it as python script
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@LaraFuhrmann @DrYak What is with this PR ? Is this already cherry-picked and in production ? |
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I am not sure about the status. @DrYak ? |
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For the revisions of the VILOCA manuscript, we had to extend the benchmarking study,