```{css, echo=FALSE} pre code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; }

```r
BiocStyle::markdown()
options(width=60, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), 
    tidy.opts=list(width.cutoff=60), tidy=TRUE)
suppressPackageStartupMessages({
    library(systemPipeR)
})

Introduction

dircwl <- list.files()
dircwl <- dircwl[-c(30:32)]
dircwl <- dircwl[4]
for(i in seq_along(dircwl)){
    print(dircwl[i])
    files <- file.path(dircwl[i], dir(dircwl[i]))
    files_path <- which(grepl(".cwl", files))
    print(files)
    for(j in files_path){
        cmdTool_path <- files[j]
        print(cmdTool_path)
        file.cwl <- file.path(dircwl[i], paste0("workflow_", basename(cmdTool_path)))
        unlink(file.cwl)
        cmdTool2wf(cmdTool_path, file.cwl, silent = FALSE)
    }
}

Targets Files

targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
targetspathPE <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")

Annotate_peaks

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "annotate_peaks/annotate_peaks.cwl", 
    input_file = "annotate_peaks/annotate_peaks.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "annotate_peaks/workflow_annotate_peaks.cwl", 
    input_file = "annotate_peaks/annotate_peaks.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1]), cmdlist(WF[1]))

BLAST

blastp

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "blast/blastp.cwl", 
    input_file = "blast/blastp.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "blast/workflow_blastp.cwl", 
    input_file = "blast/blastp.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1]), cmdlist(WF[1]))

makeblastdb

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "blast/makeblastdb.cwl", 
    input_file = "blast/makeblastdb.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "blast/workflow_makeblastdb.cwl", 
    input_file = "blast/makeblastdb.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1]), cmdlist(WF[1]))

Bowtie2

Bowtie2-index

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "bowtie2/bowtie2-index.cwl", 
    input_file = "bowtie2/bowtie2-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "bowtie2/workflow_bowtie2-index.cwl", 
    input_file = "bowtie2/bowtie2-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Run

args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
output(args)
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)

Bowtie2-mi

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "bowtie2/bowtie2-mapping-mi.cwl", 
    input_file = "bowtie2/bowtie2-mapping-mi.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "bowtie2/workflow_bowtie2-mapping-mi.cwl", 
    input_file = "bowtie2/bowtie2-mapping-mi.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Run

args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
output(args)
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)

Bowtie2-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "bowtie2/bowtie2-mapping-se.cwl", 
    input_file = "bowtie2/bowtie2-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "bowtie2/workflow_bowtie2-mapping-se.cwl", 
    input_file = "bowtie2/bowtie2-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Bowtie2-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "bowtie2/bowtie2-mapping-pe.cwl", 
    input_file = "bowtie2/bowtie2-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "bowtie2/workflow_bowtie2-mapping-pe.cwl", 
    input_file = "bowtie2/bowtie2-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

BUSCO

BUSCO

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "BUSCO/BUSCO.cwl", 
    input_file = "BUSCO/BUSCO.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "BUSCO/workflow_BUSCO.cwl", 
    input_file = "BUSCO/BUSCO.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

BWA

bwa-index

CommandLineTool

idx <- loadWF(targets = NULL, wf_file = "bwa/bwa-index.cwl", 
    input_file = "bwa/bwa-index.yml", dir_path = dir_path)
idx <- renderWF(idx)
cmdlist(idx)
output(idx[1])
runCommandline(idx, dir=FALSE)
check.output(idx)

Workflow

WF <- loadWF(targets = NULL, wf_file = "bwa/workflow_bwa-index.cwl", 
    input_file = "bwa/bwa-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(idx[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Run

WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)

bwa-aln

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-aln.cwl", 
    input_file = "bwa/bwa-aln.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-aln.cwl", 
    input_file = "bwa/bwa-aln.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Run

args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
output(args)
WF <- runCommandline(WF, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")
output(WF)

bwa-mem-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-mem-se.cwl", 
    input_file = "bwa/bwa-mem-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-mem-se.cwl", 
    input_file = "bwa/bwa-mem-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

bwa-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-se.cwl", 
    input_file = "bwa/bwa-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-se.cwl", 
    input_file = "bwa/bwa-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

bwa-samse

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "bwa/bwa-samse.cwl", 
    input_file = "bwa/bwa-samse.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "bwa/workflow_bwa-samse.cwl", 
    input_file = "bwa/bwa-samse.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

bwa-mem-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "bwa/bwa-mem-pe.cwl", 
    input_file = "bwa/bwa-mem-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "bwa/workflow_bwa-mem-pe.cwl", 
    input_file = "bwa/bwa-mem-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

bwa-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "bwa/bwa-pe.cwl", 
    input_file = "bwa/bwa-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "bwa/workflow_bwa-pe.cwl", 
    input_file = "bwa/bwa-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

count_rangesets

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "count_rangesets/count_rangesets.cwl", 
    input_file = "count_rangesets/count_rangesets.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "count_rangesets/workflow_count_rangesets.cwl", 
    input_file = "count_rangesets/count_rangesets.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(output(args), output(WF))

cutadapt

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "cutadapt/cutadapt.cwl", 
    input_file = "cutadapt/cutadapt.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "cutadapt/workflow_cutadapt.cwl", 
    input_file = "cutadapt/cutadapt.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))

example

CommandLineTool

targets_examples <- system.file("extdata", "cwl/example/targets_example.txt", package="systemPipeR")
args <- loadWF(targets = targets_examples, wf_file = "example/example.cwl", 
    input_file = "example/example.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targets_examples, wf_file = "example/workflow_example.cwl", 
    input_file = "example/example.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

fastqc

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "fastqc/fastqc-se.cwl", 
    input_file = "fastqc/fastqc-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_"))
cmdlist(args[1])
output(args[1])

Workflow

# WF <- loadWF(targets = targetspath, wf_file = "fastqc/workflow_fastqc-.cwl", 
#     input_file = "fastqc/fastqc.yml", dir_path = dir_path)
# WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_"))
# cmdlist(WF[1])
# output(WF[1])

Check

identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))

fastq-dump

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "fastq-dump/fastq-dump.cwl", 
    input_file = "fastq-dump/fastq-dump.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "fastq-dump/workflow_fastq-dump.cwl", 
    input_file = "fastq-dump/fastq-dump.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))

fastx_clipper

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "fastx_toolkit/fastx_clipper.cwl", 
    input_file = "fastx_toolkit/fastx_clipper.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "fastx_toolkit/workflow_fastx_clipper.cwl", 
    input_file = "fastx_toolkit/fastx_clipper.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args), cmdlist(WF))
identical(output(args), output(WF))

GATK

gsnap-index

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "gsnap/gsnap-index.cwl", 
    input_file = "gsnap/gsnap-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "gsnap/workflow_gsnap-index.cwl", 
    input_file = "gsnap/gsnap-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

gsnap-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "gsnap/gsnap-mapping-pe.cwl", 
    input_file = "gsnap/gsnap-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "gsnap/workflow_gsnap-mapping-pe.cwl", 
    input_file = "gsnap/gsnap-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

gunzip

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "gunzip/gunzip.cwl", 
    input_file = "gunzip/gunzip.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FILE_PATH_",
                                     SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "gunzip/workflow_gunzip.cwl", 
    input_file = "gunzip/gunzip.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_",
                                      SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

hisat2

hisat2-index

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "hisat2/hisat2-index.cwl", 
    input_file = "hisat2/hisat2-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "hisat2/workflow_hisat2-index.cwl", 
    input_file = "hisat2/hisat2-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Run

runCommandline(args, make_bam = FALSE, dir=FALSE)
runCommandline(WF, make_bam = FALSE, dir=FALSE)
runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "testing_folder")

hisat2-se

CommandLineTool

hisat2 <- loadWF(targets = targetspath, wf_file = "hisat2/hisat2-mapping-se.cwl", 
    input_file = "hisat2/hisat2-mapping-se.yml", dir_path = dir_path)
hisat2 <- renderWF(hisat2, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(hisat2[1])
output(hisat2[1])
a <- runCommandline(hisat2, make_bam = FALSE, dir=FALSE)

Workflow

WF <- loadWF(targets = targetspath, wf_file = "hisat2/workflow_hisat2-mapping-se.cwl", 
    input_file = "hisat2/hisat2-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(hisat2[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Run

args <- runCommandline(args, make_bam = FALSE, dir=FALSE)
WF <- runCommandline(WF, make_bam = FALSE)
args <- runCommandline(args, make_bam = TRUE)
WF <- runCommandline(WF, make_bam = TRUE, dir=TRUE)
WF <- runCommandline(WF, make_bam = TRUE, dir=TRUE, dir.name = "testing_folder")

hisat2-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "hisat2/hisat2-mapping-pe.cwl", 
    input_file = "hisat2/hisat2-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "hisat2/workflow_hisat2-mapping-pe.cwl", 
    input_file = "hisat2/hisat2-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Workflow hisat2 + samtools

WF <- loadWF(targets = targetspathPE, wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl", 
    input_file = "workflow-hisat2/workflow_hisat2-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])
WF <- loadWF(targets = targetspathPE, wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl", 
    input_file = "workflow-hisat2/workflow_hisat2-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

kallisto

kallisto-index

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "kallisto/kallisto-index.cwl", 
    input_file = "kallisto/kallisto.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "kallisto/workflow_kallisto-index.cwl", 
    input_file = "kallisto/kallisto.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

kallisto-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "kallisto/kallisto.cwl", 
    input_file = "kallisto/kallisto.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "kallisto/workflow_kallisto.cwl", 
    input_file = "kallisto/kallisto.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

MACS2

macs2-noinput

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "MACS2/macs2-noinput.cwl", 
    input_file = "MACS2/macs2-noinput.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "MACS2/workflow_macs2-noinput.cwl", 
    input_file = "MACS2/macs2-noinput.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

macs2-input

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "MACS2/macs2-input.cwl", 
    input_file = "MACS2/macs2-input.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "MACS2/workflow_macs2-input.cwl", 
    input_file = "MACS2/macs2-input.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

mergeBamByFactor

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "mergeBamByFactor/merge-bam.cwl", 
    input_file = "mergeBamByFactor/merge-bam.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "mergeBamByFactor/workflow_merge-bam.cwl", 
    input_file = "mergeBamByFactor/merge-bam.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_PATH_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Picard

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "picard/picard_markduplicates.cwl", 
    input_file = "picard/picard_markduplicates.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "picard/workflow_picard_markduplicates.cwl", 
    input_file = "picard/picard_markduplicates.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_SORT_PATH_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

preprocessReads

preprocessReads-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "preprocessReads/trim-se.cwl", 
    input_file = "preprocessReads/trim-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "preprocessReads/workflow_trim-se.cwl", 
    input_file = "preprocessReads/trim-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(output(args), output(WF))

preprocessReads-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "preprocessReads/trim-pe.cwl", 
    input_file = "preprocessReads/trim-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "preprocessReads/workflow_trim-pe.cwl", 
    input_file = "preprocessReads/trim-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(output(args), output(WF))

rsubread

rsubread-index

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "rsubread/rsubread-index.cwl", 
    input_file = "rsubread/rsubread-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "rsubread/workflow_rsubread-index.cwl", 
    input_file = "rsubread/rsubread-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

rsubread-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "rsubread/rsubread-mapping-se.cwl", 
    input_file = "rsubread/rsubread-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_",
                                     SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "rsubread/workflow_rsubread-mapping-se.cwl", 
    input_file = "rsubread/rsubread-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_",
                                      SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

rundiff

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "rundiff/rundiff.cwl", 
    input_file = "rundiff/rundiff.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_",
                                     SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "rundiff/workflow_rundiff.cwl", 
    input_file = "rundiff/rundiff.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_",
                                      SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(output(args), output(WF))

samtools

samtools-index

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-index.cwl", 
    input_file = "samtools/samtools-index.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_SORT_PATH_",
                                     SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-index.cwl", 
    input_file = "samtools/samtools-index.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_SORT_PATH_",
                                      SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

samtools-sort

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-sort.cwl", 
    input_file = "samtools/samtools-sort.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_BAM_PATH_",
                                     SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-sort.cwl", 
    input_file = "samtools/samtools-sort.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_BAM_PATH_",
                                      SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

samtools-view

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "samtools/samtools-view.cwl", 
    input_file = "samtools/samtools-view.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_SAM_PATH",
                                     SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "samtools/workflow_samtools-view.cwl", 
    input_file = "samtools/samtools-view.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_SAM_PATH",
                                      SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

star

star-index

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "star/star-index.cwl", 
    input_file = "star/star-index.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "star/workflow_star-index.cwl", 
    input_file = "star/star-index.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

star-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "star/star-mapping-se.cwl", 
    input_file = "star/star-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "star/workflow_star-mapping-se.cwl", 
    input_file = "star/star-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

star-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "star/star-mapping-pe.cwl", 
    input_file = "star/star-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "star/workflow_star-mapping-pe.cwl", 
    input_file = "star/star-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

test

CommandLineTool

args <- loadWF(targets = NULL, wf_file = "test/test.cwl", 
    input_file = "test/test.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = NULL, wf_file = "test/workflow_test.cwl", 
    input_file = "test/test.yml", dir_path = dir_path)
WF <- renderWF(WF)
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

tophat2

tophat2-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "tophat2/tophat2-mapping-se.cwl", 
    input_file = "tophat2/tophat2-mapping-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "tophat2/workflow_tophat2-mapping-se.cwl", 
    input_file = "tophat2/tophat2-mapping-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

tophat2-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "tophat2/tophat2-mapping-pe.cwl", 
    input_file = "tophat2/tophat2-mapping-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "tophat2/workflow_tophat2-mapping-pe.cwl", 
    input_file = "tophat2/tophat2-mapping-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

trim_galore

trim_galore-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "trim_galore/trim_galore-se.cwl", 
    input_file = "trim_galore/trim_galore-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "trim_galore/workflow_trim_galore-se.cwl", 
    input_file = "trim_galore/trim_galore-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

trim_galore-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "trim_galore/trim_galore-pe.cwl", 
    input_file = "trim_galore/trim_galore-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "trim_galore/workflow_trim_galore-pe.cwl", 
    input_file = "trim_galore/trim_galore-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Trimmomatic

trimmomatic-se

CommandLineTool

args <- loadWF(targets = targetspath, wf_file = "trimmomatic/trimmomatic-se.cwl", 
    input_file = "trimmomatic/trimmomatic-se.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspath, wf_file = "trimmomatic/workflow_trimmomatic-se.cwl", 
    input_file = "trimmomatic/trimmomatic-se.yml", dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

trimmomatic-pe

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "trimmomatic/trimmomatic-pe.cwl", 
    input_file = "trimmomatic/trimmomatic-pe.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "trimmomatic/workflow_trimmomatic-pe.cwl", 
    input_file = "trimmomatic/trimmomatic-pe.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Trinity

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "trinity/trinity.cwl", 
    input_file = "trinity/trinity.yml", dir_path = dir_path)
args <- renderWF(args)
cmdlist(args[1])
output(args[1])

Workflow

varseq

annotate

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "varseq/annotate.cwl", 
    input_file = "varseq/varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_annotate.cwl", 
    input_file = "varseq/varseq.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

combine

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "varseq/combine.cwl", 
    input_file = "varseq/varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_combine.cwl", 
    input_file = "varseq/varseq.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

filter

CommandLineTool

args <- loadWF(targets = targetspathPE, wf_file = "varseq/filter.cwl", 
    input_file = "varseq/varseq.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(args[1])
output(args[1])

Workflow

WF <- loadWF(targets = targetspathPE, wf_file = "varseq/workflow_filter.cwl", 
    input_file = "varseq/varseq.yml", dir_path = dir_path)
WF <- renderWF(WF,inputvars = c(FileName1 = "_FASTQ_PATH1_",
                                     FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
cmdlist(WF[1])
output(WF[1])

Check

identical(cmdlist(args[1])[[1]][[1]], cmdlist(WF[1])[[1]][[1]])

Worflows

Hisat2 and Samtools

WF <- loadWorkflow(targets = targetspath, wf_file = "workflow-hisat2/workflow_hisat2-se.cwl", 
                   input_file = "workflow-hisat2/workflow_hisat2-se.yml",
                   dir_path = dir_path)
WF <- renderWF(WF, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))

appendStep(sal) <- SYSargsList(targets = targetspath, wf_file = "workflow-hisat2/workflow_hisat2-se.cwl", 
                   input_file = "workflow-hisat2/workflow_hisat2-se.yml",
                   dir_path = dir_path, 
                   inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"),
                        step_name="test",
                        silent = FALSE,
                        rm_targets_col = NULL, dependency=NULL)

Run

WF1 <- runCommandline(WF, make_bam = FALSE, dir=TRUE) 
WF2 <- runCommandline(WF, make_bam = FALSE, dir=TRUE, dir.name = "test") 
parse(text="1=1")

Version Information

sessionInfo()

Funding

This project was supported by funds from the National Institutes of Health (NIH).

References



tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.