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@SunPast SunPast commented Nov 9, 2025

Add strelka, which is a variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

@Yunuuuu
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Yunuuuu commented Nov 9, 2025

StrelkaScripts are missing

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SunPast commented Nov 15, 2025

@Yunuuuu 彭老师,从Python类继承的strelka貌似不能简单使用extdata里的python脚本,会莫名声称无法定位脚本位置,可能因为它的工作原理和krakentools有区别?我尝试将 strelka 从 Python 类继承改为了 Command 类继承,在 extdata 中仍保留了 Python 脚本,并用pkg_extdata指定路径让其可调用。
但是Strelka官方居然不支持 Python3,最高只支持2.7。我目前这样处理:

command_locate = function() {
      py2 <- Sys.which("python2")
      if (py2 == "") {
        stop("Cannot locate python2. Please install it or activate a Conda environment with Python2.")
      }else{py2}

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2 participants