"SYSargs"
SYSargs-class.Rd
S4 class container for storing parameters of command-line- or R-based software.
SYSargs
instances are constructed by the systemArgs
function
from two simple tabular files: a targets
file and a param
file.
The latter is optional for workflow steps lacking command-line software.
Typically, a SYSargs
instance stores all sample-level inputs as well as
the paths to the corresponding outputs generated by command-line- or R-based
software generating sample-level output files. Each sample level input/outfile
operation uses its own SYSargs
instance. The outpaths of SYSargs
usually define the sample inputs for the next SYSargs
instance. This
connectivity is achieved by writing the outpaths with the
writeTargetsout
function to a new targets file that serves as input to
the next systemArgs
call. By chaining several SYSargs
steps
together one can construct complex workflows involving many sample-level
input/output file operations with any combination of command-line or R-based
software.
Objects can be created by calls of the form new("SYSargs", ...)
.
targetsin
:Object of class "data.frame"
storing tabular data from targets input file
targetsout
:Object of class "data.frame"
storing tabular data from targets output file
targetsheader
:Object of class "character"
storing header/comment lines of targets file
modules
:Object of class "character"
storing software versions from module system
software
:Object of class "character"
name of executable of command-line software
cores
:Object of class "numeric"
number of CPU cores to use
other
:Object of class "character"
additional arguments
reference
:Object of class "character"
path to reference genome file
results
:Object of class "character"
path to results directory
infile1
:Object of class "character"
paths to first FASTQ file
infile2
:Object of class "character"
paths to second FASTQ file if data is PE
outfile1
:Object of class "character"
paths to output files generated by command-line software
sysargs
:Object of class "character"
full commands used to execute external software
outpaths
:Object of class "character"
paths to final outputs including postprocessing by Rsamtools
signature(x = "SYSargs")
: extracts sample names
signature(x = "SYSargs")
: subsetting of class with bracket operator
signature(from = "list", to = "SYSargs")
: as(list, "SYSargs")
signature(x = "SYSargs")
: extracts data from cores
slot
signature(x = "SYSargs")
: extracts data from infile1
slot
signature(x = "SYSargs")
: extracts data from infile2
slot
signature(x = "SYSargs")
: extracts data from modules
slot
signature(x = "SYSargs")
: extracts slot names
signature(x = "SYSargs")
: extracts number of samples
signature(x = "SYSargs")
: extracts data from other
slot
signature(x = "SYSargs")
: extracts data from outfile1
slot
signature(x = "SYSargs")
: extracts data from outpath
slot
signature(x = "SYSargs")
: extracts data from reference
slot
signature(x = "SYSargs")
: extracts data from results
slot
signature(object = "SYSargs")
: summary view of SYSargs
objects
signature(x = "SYSargs")
: extracts data from software
slot
signature(x = "SYSargs")
: extracts data from targetsheader
slot
signature(x = "SYSargs")
: extracts data from targetsin
slot
signature(x = "SYSargs")
: extracts data from targetsout
slot
systemArgs
and runCommandline
showClass("SYSargs")
#> Class "SYSargs" [package "systemPipeR"]
#>
#> Slots:
#>
#> Name: targetsin targetsout targetsheader modules software
#> Class: data.frame data.frame character character character
#>
#> Name: cores other reference results infile1
#> Class: numeric character character character character
#>
#> Name: infile2 outfile1 sysargs outpaths
#> Class: character character character character
## Construct SYSargs object from param and targets files
param <- system.file("extdata", "tophat.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 'tophat' on 18 samples
names(args); targetsin(args); targetsout(args); targetsheader(args);
#> [1] "targetsin" "targetsout" "targetsheader" "modules"
#> [5] "software" "cores" "other" "reference"
#> [9] "results" "infile1" "infile2" "outfile1"
#> [13] "sysargs" "outpaths"
#> FileName SampleName Factor SampleLong Experiment
#> 1 ./data/SRR446027_1.fastq.gz M1A M1 Mock.1h.A 1
#> 2 ./data/SRR446028_1.fastq.gz M1B M1 Mock.1h.B 1
#> 3 ./data/SRR446029_1.fastq.gz A1A A1 Avr.1h.A 1
#> 4 ./data/SRR446030_1.fastq.gz A1B A1 Avr.1h.B 1
#> 5 ./data/SRR446031_1.fastq.gz V1A V1 Vir.1h.A 1
#> 6 ./data/SRR446032_1.fastq.gz V1B V1 Vir.1h.B 1
#> 7 ./data/SRR446033_1.fastq.gz M6A M6 Mock.6h.A 1
#> 8 ./data/SRR446034_1.fastq.gz M6B M6 Mock.6h.B 1
#> 9 ./data/SRR446035_1.fastq.gz A6A A6 Avr.6h.A 1
#> 10 ./data/SRR446036_1.fastq.gz A6B A6 Avr.6h.B 1
#> 11 ./data/SRR446037_1.fastq.gz V6A V6 Vir.6h.A 1
#> 12 ./data/SRR446038_1.fastq.gz V6B V6 Vir.6h.B 1
#> 13 ./data/SRR446039_1.fastq.gz M12A M12 Mock.12h.A 1
#> 14 ./data/SRR446040_1.fastq.gz M12B M12 Mock.12h.B 1
#> 15 ./data/SRR446041_1.fastq.gz A12A A12 Avr.12h.A 1
#> 16 ./data/SRR446042_1.fastq.gz A12B A12 Avr.12h.B 1
#> 17 ./data/SRR446043_1.fastq.gz V12A V12 Vir.12h.A 1
#> 18 ./data/SRR446044_1.fastq.gz V12B V12 Vir.12h.B 1
#> Date
#> 1 23-Mar-2012
#> 2 23-Mar-2012
#> 3 23-Mar-2012
#> 4 23-Mar-2012
#> 5 23-Mar-2012
#> 6 23-Mar-2012
#> 7 23-Mar-2012
#> 8 23-Mar-2012
#> 9 23-Mar-2012
#> 10 23-Mar-2012
#> 11 23-Mar-2012
#> 12 23-Mar-2012
#> 13 23-Mar-2012
#> 14 23-Mar-2012
#> 15 23-Mar-2012
#> 16 23-Mar-2012
#> 17 23-Mar-2012
#> 18 23-Mar-2012
#> FileName
#> 1 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446027_1.fastq.gz.tophat/accepted_hits.bam
#> 2 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446028_1.fastq.gz.tophat/accepted_hits.bam
#> 3 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446029_1.fastq.gz.tophat/accepted_hits.bam
#> 4 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446030_1.fastq.gz.tophat/accepted_hits.bam
#> 5 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446031_1.fastq.gz.tophat/accepted_hits.bam
#> 6 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446032_1.fastq.gz.tophat/accepted_hits.bam
#> 7 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446033_1.fastq.gz.tophat/accepted_hits.bam
#> 8 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446034_1.fastq.gz.tophat/accepted_hits.bam
#> 9 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446035_1.fastq.gz.tophat/accepted_hits.bam
#> 10 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446036_1.fastq.gz.tophat/accepted_hits.bam
#> 11 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446037_1.fastq.gz.tophat/accepted_hits.bam
#> 12 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446038_1.fastq.gz.tophat/accepted_hits.bam
#> 13 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446039_1.fastq.gz.tophat/accepted_hits.bam
#> 14 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446040_1.fastq.gz.tophat/accepted_hits.bam
#> 15 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446041_1.fastq.gz.tophat/accepted_hits.bam
#> 16 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446042_1.fastq.gz.tophat/accepted_hits.bam
#> 17 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446043_1.fastq.gz.tophat/accepted_hits.bam
#> 18 /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446044_1.fastq.gz.tophat/accepted_hits.bam
#> SampleName Factor SampleLong Experiment Date
#> 1 M1A M1 Mock.1h.A 1 23-Mar-2012
#> 2 M1B M1 Mock.1h.B 1 23-Mar-2012
#> 3 A1A A1 Avr.1h.A 1 23-Mar-2012
#> 4 A1B A1 Avr.1h.B 1 23-Mar-2012
#> 5 V1A V1 Vir.1h.A 1 23-Mar-2012
#> 6 V1B V1 Vir.1h.B 1 23-Mar-2012
#> 7 M6A M6 Mock.6h.A 1 23-Mar-2012
#> 8 M6B M6 Mock.6h.B 1 23-Mar-2012
#> 9 A6A A6 Avr.6h.A 1 23-Mar-2012
#> 10 A6B A6 Avr.6h.B 1 23-Mar-2012
#> 11 V6A V6 Vir.6h.A 1 23-Mar-2012
#> 12 V6B V6 Vir.6h.B 1 23-Mar-2012
#> 13 M12A M12 Mock.12h.A 1 23-Mar-2012
#> 14 M12B M12 Mock.12h.B 1 23-Mar-2012
#> 15 A12A A12 Avr.12h.A 1 23-Mar-2012
#> 16 A12B A12 Avr.12h.B 1 23-Mar-2012
#> 17 V12A V12 Vir.12h.A 1 23-Mar-2012
#> 18 V12B V12 Vir.12h.B 1 23-Mar-2012
#> [1] "# Project ID: Arabidopsis - Pseudomonas alternative splicing study (SRA: SRP010938; PMID: 24098335)"
#> [2] "# The following line(s) allow to specify the contrasts needed for comparative analyses, such as DEG identification. All possible comparisons can be specified with 'CMPset: ALL'."
#> [3] "# <CMP> CMPset1: M1-A1, M1-V1, A1-V1, M6-A6, M6-V6, A6-V6, M12-A12, M12-V12, A12-V12"
#> [4] "# <CMP> CMPset2: ALL"
software(args); modules(args); cores(args); outpaths(args)
#> [1] "tophat"
#> [1] "bowtie2/2.2.5" "tophat/2.0.14"
#> [1] 4
#> M1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446027_1.fastq.gz.tophat/accepted_hits.bam"
#> M1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446028_1.fastq.gz.tophat/accepted_hits.bam"
#> A1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446029_1.fastq.gz.tophat/accepted_hits.bam"
#> A1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446030_1.fastq.gz.tophat/accepted_hits.bam"
#> V1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446031_1.fastq.gz.tophat/accepted_hits.bam"
#> V1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446032_1.fastq.gz.tophat/accepted_hits.bam"
#> M6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446033_1.fastq.gz.tophat/accepted_hits.bam"
#> M6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446034_1.fastq.gz.tophat/accepted_hits.bam"
#> A6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446035_1.fastq.gz.tophat/accepted_hits.bam"
#> A6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446036_1.fastq.gz.tophat/accepted_hits.bam"
#> V6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446037_1.fastq.gz.tophat/accepted_hits.bam"
#> V6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446038_1.fastq.gz.tophat/accepted_hits.bam"
#> M12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446039_1.fastq.gz.tophat/accepted_hits.bam"
#> M12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446040_1.fastq.gz.tophat/accepted_hits.bam"
#> A12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446041_1.fastq.gz.tophat/accepted_hits.bam"
#> A12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446042_1.fastq.gz.tophat/accepted_hits.bam"
#> V12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446043_1.fastq.gz.tophat/accepted_hits.bam"
#> V12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446044_1.fastq.gz.tophat/accepted_hits.bam"
sysargs(args); other(args); reference(args); results(args); infile1(args)
#> M1A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446027_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446027_1.fastq.gz "
#> M1B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446028_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446028_1.fastq.gz "
#> A1A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446029_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446029_1.fastq.gz "
#> A1B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446030_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446030_1.fastq.gz "
#> V1A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446031_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446031_1.fastq.gz "
#> V1B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446032_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446032_1.fastq.gz "
#> M6A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446033_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446033_1.fastq.gz "
#> M6B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446034_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446034_1.fastq.gz "
#> A6A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446035_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446035_1.fastq.gz "
#> A6B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446036_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446036_1.fastq.gz "
#> V6A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446037_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446037_1.fastq.gz "
#> V6B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446038_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446038_1.fastq.gz "
#> M12A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446039_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446039_1.fastq.gz "
#> M12B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446040_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446040_1.fastq.gz "
#> A12A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446041_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446041_1.fastq.gz "
#> A12B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446042_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446042_1.fastq.gz "
#> V12A
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446043_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446043_1.fastq.gz "
#> V12B
#> "tophat -p 4 -g 1 --segment-length 25 -i 30 -I 3000 -o /home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446044_1.fastq.gz.tophat /home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta ./data/SRR446044_1.fastq.gz "
#> [1] "-g 1 --segment-length 25 -i 30 -I 3000"
#> [1] "/home/runner/work/systemPipeR/systemPipeR/docs/reference/data/tair10.fasta"
#> [1] "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/"
#> M1A M1B
#> "./data/SRR446027_1.fastq.gz" "./data/SRR446028_1.fastq.gz"
#> A1A A1B
#> "./data/SRR446029_1.fastq.gz" "./data/SRR446030_1.fastq.gz"
#> V1A V1B
#> "./data/SRR446031_1.fastq.gz" "./data/SRR446032_1.fastq.gz"
#> M6A M6B
#> "./data/SRR446033_1.fastq.gz" "./data/SRR446034_1.fastq.gz"
#> A6A A6B
#> "./data/SRR446035_1.fastq.gz" "./data/SRR446036_1.fastq.gz"
#> V6A V6B
#> "./data/SRR446037_1.fastq.gz" "./data/SRR446038_1.fastq.gz"
#> M12A M12B
#> "./data/SRR446039_1.fastq.gz" "./data/SRR446040_1.fastq.gz"
#> A12A A12B
#> "./data/SRR446041_1.fastq.gz" "./data/SRR446042_1.fastq.gz"
#> V12A V12B
#> "./data/SRR446043_1.fastq.gz" "./data/SRR446044_1.fastq.gz"
infile2(args); outfile1(args); SampleName(args)
#> M1A M1B A1A A1B V1A V1B M6A M6B A6A A6B V6A V6B M12A M12B A12A A12B
#> "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
#> V12A V12B
#> "" ""
#> M1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446027_1.fastq.gz.tophat"
#> M1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446028_1.fastq.gz.tophat"
#> A1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446029_1.fastq.gz.tophat"
#> A1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446030_1.fastq.gz.tophat"
#> V1A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446031_1.fastq.gz.tophat"
#> V1B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446032_1.fastq.gz.tophat"
#> M6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446033_1.fastq.gz.tophat"
#> M6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446034_1.fastq.gz.tophat"
#> A6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446035_1.fastq.gz.tophat"
#> A6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446036_1.fastq.gz.tophat"
#> V6A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446037_1.fastq.gz.tophat"
#> V6B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446038_1.fastq.gz.tophat"
#> M12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446039_1.fastq.gz.tophat"
#> M12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446040_1.fastq.gz.tophat"
#> A12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446041_1.fastq.gz.tophat"
#> A12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446042_1.fastq.gz.tophat"
#> V12A
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446043_1.fastq.gz.tophat"
#> V12B
#> "/home/runner/work/systemPipeR/systemPipeR/docs/reference/results/SRR446044_1.fastq.gz.tophat"
#> [1] "M1A" "M1B" "A1A" "A1B" "V1A" "V1B" "M6A" "M6B" "A6A" "A6B"
#> [11] "V6A" "V6B" "M12A" "M12B" "A12A" "A12B" "V12A" "V12B"
## Return sample comparisons
readComp(args, format = "vector", delim = "-")
#> $CMPset1
#> [1] "M1-A1" "M1-V1" "A1-V1" "M6-A6" "M6-V6" "A6-V6" "M12-A12"
#> [8] "M12-V12" "A12-V12"
#>
#> $CMPset2
#> [1] "M1-A1" "M1-V1" "M1-M6" "M1-A6" "M1-V6" "M1-M12" "M1-A12"
#> [8] "M1-V12" "A1-V1" "A1-M6" "A1-A6" "A1-V6" "A1-M12" "A1-A12"
#> [15] "A1-V12" "V1-M6" "V1-A6" "V1-V6" "V1-M12" "V1-A12" "V1-V12"
#> [22] "M6-A6" "M6-V6" "M6-M12" "M6-A12" "M6-V12" "A6-V6" "A6-M12"
#> [29] "A6-A12" "A6-V12" "V6-M12" "V6-A12" "V6-V12" "M12-A12" "M12-V12"
#> [36] "A12-V12"
#>
## The subsetting operator '[' allows to select specific samples
args[1:4]
#> An instance of 'SYSargs' for running 'tophat' on 4 samples
if (FALSE) {
## Execute SYSargs on single machine
runCommandline(args=args)
## Execute SYSargs on multiple machines
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(args),
memory="mem=10gb", time="walltime=20:00:00")
qsubRun(appfct="runCommandline(args=args)", appargs=args, qsubargs=qsubargs,
Nqsubs=1, submitdir="results", package="systemPipeR")
## Write outpaths to new targets file for next SYSargs step
writeTargetsout(x=args, file="default")
}