runCommandline.RdFunction to execute system parameters specified in SYSargs
and SYSargs2 object.
runCommandline(args, runid = "01", make_bam = FALSE, del_sam=TRUE, dir = TRUE,
dir.name = NULL, force=FALSE, input_targets = NULL, ...)object of class SYSargs or SYSargs2.
Run identifier used for log file to track system call commands.
Default is "01".
Auto-detects SAM file outputs and converts them to sorted and indexed BAM
files. Default is make_bam=FALSE.
This option allows deleting the SAM files created when the make_BAM
converts the SAM files to sorted and indexed BAM files.
Default is del_sam=TRUE.
This option allows creating an exclusive results folder for each step in the
workflow and a sub-folder for each sample defined in the targets file.
All the outputs and log files for the particular step will be created in the
respective folders. Default is dir=TRUE. Option available only for an
object of class SYSargs2.
Name of the workflow directory. Default is dir.name=FALSE. Note: This
argument is required when the dir=TRUE.
Internally, the function checks if the expected output files exist,
and it skips the command lines when the respective files exist. If the
argument force is set to TRUE, the command line will be
executed and the files overwrite. Default is force=FALSE.
This option allows selecting which targets file and, by consequence which
command line will be executed. Default is NULL, in which all command
lines will be executed.
Additional arguments to pass on to runCommandline().
Output files, their paths can be obtained with outpaths() from
SYSargs container or output() from SYSargs2.
In addition, a character vector is returned containing the same
paths.
##########################################
## Examples with \code{SYSargs2} object ##
##########################################
## Construct SYSargs2 object from CWl param, CWL input, and targets files
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
WF <- loadWorkflow(targets=targets, wf_file="hisat2/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_"))
WF
#> Instance of 'SYSargs2':
#> Slot names/accessors:
#> targets: 18 (M1A...V12B), targetsheader: 4 (lines)
#> modules: 1
#> wf: 0, clt: 1, yamlinput: 7 (inputs)
#> input: 18, output: 18
#> cmdlist: 18
#> Sub Steps:
#> 1. hisat2-mapping-se (rendered: TRUE)
#>
#>
names(WF); modules(WF); targets(WF)[1]; cmdlist(WF)[1:2]; output(WF)
#> [1] "targets" "targetsheader" "modules"
#> [4] "wf" "clt" "yamlinput"
#> [7] "cmdlist" "input" "output"
#> [10] "files" "inputvars" "cmdToCwl"
#> [13] "status" "internal_outfiles"
#> module1
#> "hisat2/2.1.0"
#> $M1A
#> $M1A$FileName
#> [1] "./data/SRR446027_1.fastq.gz"
#>
#> $M1A$SampleName
#> [1] "M1A"
#>
#> $M1A$Factor
#> [1] "M1"
#>
#> $M1A$SampleLong
#> [1] "Mock.1h.A"
#>
#> $M1A$Experiment
#> [1] 1
#>
#> $M1A$Date
#> [1] "23-Mar-2012"
#>
#>
#> $M1A
#> $M1A$`hisat2-mapping-se`
#> [1] "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446027_1.fastq.gz --threads 4"
#>
#>
#> $M1B
#> $M1B$`hisat2-mapping-se`
#> [1] "hisat2 -S ./results/M1B.sam -x ./data/tair10.fasta -k 1 --min-intronlen 30 --max-intronlen 3000 -U ./data/SRR446028_1.fastq.gz --threads 4"
#>
#>
#> $M1A
#> $M1A$`hisat2-mapping-se`
#> [1] "./results/M1A.sam"
#>
#>
#> $M1B
#> $M1B$`hisat2-mapping-se`
#> [1] "./results/M1B.sam"
#>
#>
#> $A1A
#> $A1A$`hisat2-mapping-se`
#> [1] "./results/A1A.sam"
#>
#>
#> $A1B
#> $A1B$`hisat2-mapping-se`
#> [1] "./results/A1B.sam"
#>
#>
#> $V1A
#> $V1A$`hisat2-mapping-se`
#> [1] "./results/V1A.sam"
#>
#>
#> $V1B
#> $V1B$`hisat2-mapping-se`
#> [1] "./results/V1B.sam"
#>
#>
#> $M6A
#> $M6A$`hisat2-mapping-se`
#> [1] "./results/M6A.sam"
#>
#>
#> $M6B
#> $M6B$`hisat2-mapping-se`
#> [1] "./results/M6B.sam"
#>
#>
#> $A6A
#> $A6A$`hisat2-mapping-se`
#> [1] "./results/A6A.sam"
#>
#>
#> $A6B
#> $A6B$`hisat2-mapping-se`
#> [1] "./results/A6B.sam"
#>
#>
#> $V6A
#> $V6A$`hisat2-mapping-se`
#> [1] "./results/V6A.sam"
#>
#>
#> $V6B
#> $V6B$`hisat2-mapping-se`
#> [1] "./results/V6B.sam"
#>
#>
#> $M12A
#> $M12A$`hisat2-mapping-se`
#> [1] "./results/M12A.sam"
#>
#>
#> $M12B
#> $M12B$`hisat2-mapping-se`
#> [1] "./results/M12B.sam"
#>
#>
#> $A12A
#> $A12A$`hisat2-mapping-se`
#> [1] "./results/A12A.sam"
#>
#>
#> $A12B
#> $A12B$`hisat2-mapping-se`
#> [1] "./results/A12B.sam"
#>
#>
#> $V12A
#> $V12A$`hisat2-mapping-se`
#> [1] "./results/V12A.sam"
#>
#>
#> $V12B
#> $V12B$`hisat2-mapping-se`
#> [1] "./results/V12B.sam"
#>
#>
if (FALSE) {
## Execute SYSargs2 on single machine
WF <- runCommandline(args=WF)
## Execute SYSargs on multiple machines of a compute cluster.
file.copy(system.file("extdata", ".batchtools.conf.R",
package="systemPipeR"), ".")
file.copy(system.file("extdata", "batchtools.slurm.tmpl",
package="systemPipeR"), ".")
resources <- list(walltime=120, ntasks=1, ncpus=4, memory=1024)
reg <- clusterRun(WF, FUN = runCommandline,
more.args = list(args = WF, make_bam = TRUE),
conffile=".batchtools.conf.R", template="batchtools.slurm.tmpl",
Njobs=18, runid="01", resourceList=resources)
## Monitor progress of submitted jobs
getStatus(reg=reg)
## Updates the path in the object \code{output(WF)}
WF <- output_update(WF, dir=FALSE, replace=TRUE, extension=c(".sam", ".bam"))
## Alignment stats
read_statsDF <- alignStats(WF)
read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
write.table(read_statsDF, "results/alignStats.xls",
row.names=FALSE, quote=FALSE, sep="\t")
}
#########################################
## Examples with \code{SYSargs} object ##
#########################################
## Construct SYSargs object from param and targets files
param <- system.file("extdata", "hisat2.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
#> Warning: path[1]="./data/SRR446027_1.fastq.gz": No such file or directory
#> Warning: path[2]="./data/SRR446028_1.fastq.gz": No such file or directory
#> Warning: path[3]="./data/SRR446029_1.fastq.gz": No such file or directory
#> Warning: path[4]="./data/SRR446030_1.fastq.gz": No such file or directory
#> Warning: path[5]="./data/SRR446031_1.fastq.gz": No such file or directory
#> Warning: path[6]="./data/SRR446032_1.fastq.gz": No such file or directory
#> Warning: path[7]="./data/SRR446033_1.fastq.gz": No such file or directory
#> Warning: path[8]="./data/SRR446034_1.fastq.gz": No such file or directory
#> Warning: path[9]="./data/SRR446035_1.fastq.gz": No such file or directory
#> Warning: path[10]="./data/SRR446036_1.fastq.gz": No such file or directory
#> Warning: path[11]="./data/SRR446037_1.fastq.gz": No such file or directory
#> Warning: path[12]="./data/SRR446038_1.fastq.gz": No such file or directory
#> Warning: path[13]="./data/SRR446039_1.fastq.gz": No such file or directory
#> Warning: path[14]="./data/SRR446040_1.fastq.gz": No such file or directory
#> Warning: path[15]="./data/SRR446041_1.fastq.gz": No such file or directory
#> Warning: path[16]="./data/SRR446042_1.fastq.gz": No such file or directory
#> Warning: path[17]="./data/SRR446043_1.fastq.gz": No such file or directory
#> Warning: path[18]="./data/SRR446044_1.fastq.gz": No such file or directory
args
#> An instance of 'SYSargs' for running 'hisat2' on 18 samples
names(args); modules(args); cores(args); outpaths(args); sysargs(args)
#> [1] "targetsin" "targetsout" "targetsheader" "modules"
#> [5] "software" "cores" "other" "reference"
#> [9] "results" "infile1" "infile2" "outfile1"
#> [13] "sysargs" "outpaths"
#> [1] "hisat2/2.1.0"
#> [1] 4
#> M1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446027_1.fastq.gz.hisat.bam"
#> M1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446028_1.fastq.gz.hisat.bam"
#> A1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446029_1.fastq.gz.hisat.bam"
#> A1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446030_1.fastq.gz.hisat.bam"
#> V1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446031_1.fastq.gz.hisat.bam"
#> V1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446032_1.fastq.gz.hisat.bam"
#> M6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446033_1.fastq.gz.hisat.bam"
#> M6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446034_1.fastq.gz.hisat.bam"
#> A6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446035_1.fastq.gz.hisat.bam"
#> A6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446036_1.fastq.gz.hisat.bam"
#> V6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446037_1.fastq.gz.hisat.bam"
#> V6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446038_1.fastq.gz.hisat.bam"
#> M12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446039_1.fastq.gz.hisat.bam"
#> M12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446040_1.fastq.gz.hisat.bam"
#> A12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446041_1.fastq.gz.hisat.bam"
#> A12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446042_1.fastq.gz.hisat.bam"
#> V12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446043_1.fastq.gz.hisat.bam"
#> V12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446044_1.fastq.gz.hisat.bam"
#> M1A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446027_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446027_1.fastq.gz "
#> M1B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446028_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446028_1.fastq.gz "
#> A1A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446029_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446029_1.fastq.gz "
#> A1B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446030_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446030_1.fastq.gz "
#> V1A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446031_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446031_1.fastq.gz "
#> V1B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446032_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446032_1.fastq.gz "
#> M6A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446033_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446033_1.fastq.gz "
#> M6B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446034_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446034_1.fastq.gz "
#> A6A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446035_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446035_1.fastq.gz "
#> A6B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446036_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446036_1.fastq.gz "
#> V6A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446037_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446037_1.fastq.gz "
#> V6B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446038_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446038_1.fastq.gz "
#> M12A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446039_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446039_1.fastq.gz "
#> M12B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446040_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446040_1.fastq.gz "
#> A12A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446041_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446041_1.fastq.gz "
#> A12B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446042_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446042_1.fastq.gz "
#> V12A
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446043_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446043_1.fastq.gz "
#> V12B
#> "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446044_1.fastq.gz.hisat.sam /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta -U ./data/SRR446044_1.fastq.gz "
if (FALSE) {
## Execute SYSargs on single machine
runCommandline(args=args)
## Execute SYSargs on multiple machines of a compute cluster.
file.copy(system.file("extdata", ".batchtools.conf.R", package="systemPipeR"), ".")
file.copy(system.file("extdata", "batchtools.slurm.tmpl", package="systemPipeR"), ".")
resources <- list(walltime=120, ntasks=1, ncpus=cores(args), memory=1024)
reg <- clusterRun(args, FUN = runCommandline, conffile=".batchtools.conf.R",
template="batchtools.slurm.tmpl", Njobs=18,
runid="01", resourceList=resources)
## Monitor progress of submitted jobs
getStatus(reg=reg)
file.exists(outpaths(args))
## Alignment stats
read_statsDF <- alignStats(args)
read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE,
quote=FALSE, sep="\t")
}