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Klinische Genetica
capture-lumc
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13
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41
Pipeline cannot handle spaces in sample names
Bug
Speed up pipeline by using latest version of cutadapt
Improvement
Speed up
Make BQSR variants optional
Improvement
Covstats with different ROIs per sample
Look into minimap2 as potential aligner
Add wildcard for pre and postqc so fast-count rules can be one rule
Add wildcard for r1 and r2 so merge and seqtk rules can be one rule
Look into using picard metrics in stead of calculating our own mapping statistics
Pipeline configuration file in stead of --config values
Update cutadapt to version 1.15 for multicore support