sysargs.RdMethods to access information from SYSargs object.
sysargs(x)object of class SYSargs
various outputs
## 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 "