## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("RcwlPipelines") ## ----getDevel, eval=FALSE----------------------------------------------------- # BiocManager::install("rworkflow/RcwlPipelines") ## ----Load, message=FALSE------------------------------------------------------ library(RcwlPipelines) ## ----------------------------------------------------------------------------- ## For vignette use only. users don't need to do this step. Sys.setenv(cachePath = tempdir()) ## ---- message=FALSE----------------------------------------------------------- atls <- cwlUpdate(branch = "dev") ## sync the tools/pipelines. atls table(mcols(atls)$Type) ## ----------------------------------------------------------------------------- t1 <- cwlSearch(c("bwa", "mem")) t1 mcols(t1) ## ----------------------------------------------------------------------------- bwa <- cwlLoad(title(t1)[1]) ## "tl_bwa" bwa <- cwlLoad(mcols(t1)$fpath[1]) ## equivalent to the above. bwa ## ---- warning=FALSE----------------------------------------------------------- rnaseq_Sf <- cwlLoad("pl_rnaseq_Sf") plotCWL(rnaseq_Sf) ## ----------------------------------------------------------------------------- arguments(rnaseq_Sf, "STAR")[5:6] arguments(rnaseq_Sf, "STAR")[[6]] <- 5 arguments(rnaseq_Sf, "STAR")[5:6] ## ----------------------------------------------------------------------------- searchContainer("STAR", repo = "biocontainers", source = "quay") ## ----------------------------------------------------------------------------- requirements(rnaseq_Sf, "STAR")[[1]] requirements(rnaseq_Sf, "STAR")[[1]] <- requireDocker( docker = "quay.io/biocontainers/star:2.7.8a--0") requirements(rnaseq_Sf, "STAR")[[1]] ## ---- eval=FALSE-------------------------------------------------------------- # inputs(rnaseq_Sf) # rnaseq_Sf$in_seqfiles <- list("sample_R1.fq.gz", # "sample_R2.fq.gz") # rnaseq_Sf$in_prefix <- "sample" # rnaseq_Sf$in_genomeDir <- "genome_STAR_index_Dir" # rnaseq_Sf$in_GTFfile <- "GENCODE_version.gtf" # # runCWL(rnaseq_Sf, outdir = "output/sample", docker = TRUE) ## ---- eval=FALSE-------------------------------------------------------------- # library(BioParallel) # bpparam <- BatchtoolsParam(workers = 2, cluster = "sge", # template = batchtoolsTemplate("sge")) # # inputList <- list(in_seqfiles = list(sample1 = list("sample1_R1.fq.gz", # "sample1_R2.fq.gz"), # sample2 = list("sample2_R1.fq.gz", # "sample2_R2.fq.gz")), # in_prefix = list(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()