# #设置,包括= FALSE --------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- eval = FALSE -------------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages (BiocManager) # BiocManager::安装(“RcwlPipelines ") ## ---- getDevel eval = FALSE ----------------------------------------------------- # BiocManager::安装(“rworkflow / RcwlPipelines ") ## ---- 加载消息= FALSE ------------------------------------------------------ 库(RcwlPipelines ) ## ----------------------------------------------------------------------------- ## 仅供装饰图案使用。用户不需要执行此步骤。Sys。setenv (cachePath = tempdir ()) ## ---- 消息= FALSE ----------------------------------------------------------- atl < - cwlUpdate(分支= dev) # #同步工具/管道。atl表(mcols美元(atl)类型 ) ## ----------------------------------------------------------------------------- t1 < - cwlSearch (c(“bwa”、“mem)) t1 mcols (t1 ) ## ----------------------------------------------------------------------------- bwa < - cwlLoad(标题(t1)[1]) # #“tl_bwa bwa < - cwlLoad (mcols fpath美元(t1)[1]) # #相当于上面。bwa # #——警告= FALSE ----------------------------------------------------------- rnaseq_Sf < - cwlLoad plotCWL (rnaseq_Sf(“pl_rnaseq_Sf”) ) ## ----------------------------------------------------------------------------- 参数(rnaseq_Sf,“明星”)[5:6]参数(rnaseq_Sf,“明星”)[[6]]< - 5参数(rnaseq_Sf,“明星”)[5:6 ] ## ----------------------------------------------------------------------------- 回购= searchContainer(“明星”、“biocontainers”,源= "码头 ") ## ----------------------------------------------------------------------------- 需求(rnaseq_Sf,“明星”)([1])需求(rnaseq_Sf,“明星”)[[1]]< - requireDocker(码头工人=“quay.io / biocontainers /明星:2.7.8a——0”)要求(rnaseq_Sf,“明星”)[[1 ]] ## ---- eval = FALSE -------------------------------------------------------------- # 输入(rnaseq_Sf) # rnaseq_Sf in_seqfiles < -列表(“sample_R1.fq.gz”,# rnaseq_Sf$in_prefix <- "sample" # rnaseq_Sf$in_genomeDir <- "genome_STAR_index_Dir" # rnaseq_Sf$in_GTFfile <- "GENCODE_version. gz")“# # runCWL gtf (rnaseq_Sf outdir =“输出/样本”,码头工人= TRUE ) ## ---- eval = FALSE -------------------------------------------------------------- # 库(BioParallel) # bpparam < - BatchtoolsParam(工人= 2,集群=“白银”,#模板= batchtoolsTemplate(“白银”))# # inputList < -列表(in_seqfiles =列表(sample1 =列表(“sample1_R1.fq.gz”#“sample1_R2.fq.gz”),# sample2 =列表(“sample2_R1.fq.gz”#“sample2_R2.fq.gz”)),# in_prefix =列表(sample1 =“sample1”, # sample2 = "sample2")) # # paramList <- list(in_genomeDir = "genome_STAR_index_Dir", # in_GTFfile = "GENCODE_version.gtf", # in_runThreadN = 16) # # runCWLBatch(rnaseq_Sf, outdir = "output", # inputList, paramList, # BPPARAM = bpparam) ## ----------------------------------------------------------------------------- sessionInfo()