createParam V1
suppressPackageStartupMessages({
library(systemPipeR)
})
createParam by default uses the version 1 syntax, so there is no need to
provide additional version argument. We will see in the next section how to
use syntaxVersion to change to the v2 syntax.
Input
Imagine we want to create CWL for command:
hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz
To use createParam, simply write the command in a pseudo-bash script format:
command <- "
hisat2 \
-S <F, out: ./results/M1A.sam> \
-x <F: ./data/tair10.fasta> \
-k <int: 1> \
-min-intronlen <int: 30> \
-max-intronlen <int: 3000> \
-threads <int: 4> \
-U <F: ./data/SRR446027_1.fastq.gz>
"
Format
What does the string above mean?
-
First line is the base command. Each line is an argument with its default value.
-
For argument lines (starting from the second line), any word before the first space with leading
-or--in each will be treated as a prefix, like-Sor--min. Any line without this first word will be treated as no prefix. -
All defaults are placed inside
<...>. -
First argument is the input argument type. “File” (or “F”) for files, “int” for integers, “string” for character strings.
-
Optional: use the keyword
outfollowed the type with a,comma separation to indicate if this argument is also an CWL output. -
Then, use
:to separate keywords and default values, any non-space value after the:will be treated as the default value. -
If any argument has no default value, just a flag, like
--verbose, there is no need to add any<...>
run createParam Function
The string above that we just defined will be used as input for createParam.
If the format is correct, after parsing, the function will print the three components of the cwl file:
- BaseCommand: Specifies the program to execute.
- Inputs: Defines the input parameters of the process.
- Outputs: Defines the parameters representing the output of the process.
The fourth printed component is the translated command-line from CWL.
If in you are using R interactively, the function will verify that everything is correct and will ask you to proceed. Here, the user can answer “no” and provide more information at the string level. Another question is to save the param created here.
If running the workflow in non-interactive mode, the createParam function will
consider “yes” and returning the container.
cmd <- createParam(command, writeParamFiles = FALSE)
## *****BaseCommand*****
## hisat2
## *****Inputs*****
## S:
## type: File
## preF: -S
## yml: ./results/M1A.sam
## x:
## type: File
## preF: -x
## yml: ./data/tair10.fasta
## k:
## type: int
## preF: -k
## yml: 1
## min-intronlen:
## type: int
## preF: -min-intronlen
## yml: 30
## max-intronlen:
## type: int
## preF: -max-intronlen
## yml: 3000
## threads:
## type: int
## preF: -threads
## yml: 4
## U:
## type: File
## preF: -U
## yml: ./data/SRR446027_1.fastq.gz
## *****Outputs*****
## output1:
## type: File
## value: ./results/M1A.sam
## *****Parsed raw command line*****
## hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz
If the user chooses not to save the param files on the above operation,
later, one can use the writeParamFiles function.
writeParamFiles(cmd, overwrite = TRUE)
## Written content of 'commandLine' to file:
## param/cwl/hisat2/hisat2.cwl
## Written content of 'commandLine' to file:
## param/cwl/hisat2/hisat2.yml
By default, the files will be saved inside ./param/cwl/base_cmd. It means a
child folder under param then cwl, and create a new folder named by the base command
of the command-line.
Access and edit param files
Print a component
printParam(cmd, position = "baseCommand") ## Print a baseCommand section
## *****BaseCommand*****
## hisat2
printParam(cmd, position = "outputs")
## *****Outputs*****
## output1:
## type: File
## value: ./results/M1A.sam
printParam(cmd, position = "inputs", index = 1:2) ## Print by index
## *****Inputs*****
## S:
## type: File
## preF: -S
## yml: ./results/M1A.sam
## x:
## type: File
## preF: -x
## yml: ./data/tair10.fasta
printParam(cmd, position = "inputs", index = -1:-2) ## Negative indexing printing to exclude certain indices in a position
## *****Inputs*****
## k:
## type: int
## preF: -k
## yml: 1
## min-intronlen:
## type: int
## preF: -min-intronlen
## yml: 30
## max-intronlen:
## type: int
## preF: -max-intronlen
## yml: 3000
## threads:
## type: int
## preF: -threads
## yml: 4
## U:
## type: File
## preF: -U
## yml: ./data/SRR446027_1.fastq.gz
Subsetting the command-line
cmd2 <- subsetParam(cmd, position = "inputs", index = 1:2, trim = TRUE)
## *****Inputs*****
## S:
## type: File
## preF: -S
## yml: ./results/M1A.sam
## x:
## type: File
## preF: -x
## yml: ./data/tair10.fasta
## *****Parsed raw command line*****
## hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta
cmdlist(cmd2)
## $defaultid
## $defaultid$hisat2
## [1] "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta"
cmd2 <- subsetParam(cmd, position = "inputs", index = c("S", "x"), trim = TRUE)
## *****Inputs*****
## S:
## type: File
## preF: -S
## yml: ./results/M1A.sam
## x:
## type: File
## preF: -x
## yml: ./data/tair10.fasta
## *****Parsed raw command line*****
## hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta
cmdlist(cmd2)
## $defaultid
## $defaultid$hisat2
## [1] "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta"
Replacing a existing argument in the command-line
cmd3 <- replaceParam(cmd, "base", index = 1, replace = list(baseCommand = "bwa"))
## Replacing baseCommand
## *****BaseCommand*****
## bwa
## *****Parsed raw command line*****
## bwa -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz
cmdlist(cmd3)
## $defaultid
## $defaultid$hisat2
## [1] "bwa -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz"
new_inputs <- new_inputs <- list(
"new_input1" = list(type = "File", preF="-b", yml ="myfile"),
"new_input2" = "-L <int: 4>"
)
cmd4 <- replaceParam(cmd, "inputs", index = 1:2, replace = new_inputs)
## Replacing inputs
## *****Inputs*****
## new_input1:
## type: File
## preF: -b
## yml: myfile
## new_input2:
## type: int
## preF: -L
## yml: 4
## k:
## type: int
## preF: -k
## yml: 1
## min-intronlen:
## type: int
## preF: -min-intronlen
## yml: 30
## max-intronlen:
## type: int
## preF: -max-intronlen
## yml: 3000
## threads:
## type: int
## preF: -threads
## yml: 4
## U:
## type: File
## preF: -U
## yml: ./data/SRR446027_1.fastq.gz
## *****Parsed raw command line*****
## hisat2 -b myfile -L 4 -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz
cmdlist(cmd4)
## $defaultid
## $defaultid$hisat2
## [1] "hisat2 -b myfile -L 4 -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz"
Adding new arguments
newIn <- new_inputs <- list(
"new_input1" = list(type = "File", preF="-b1", yml ="myfile1"),
"new_input2" = list(type = "File", preF="-b2", yml ="myfile2"),
"new_input3" = "-b3 <F: myfile3>"
)
cmd5 <- appendParam(cmd, "inputs", index = 1:2, append = new_inputs)
## Replacing inputs
## *****Inputs*****
## S:
## type: File
## preF: -S
## yml: ./results/M1A.sam
## x:
## type: File
## preF: -x
## yml: ./data/tair10.fasta
## k:
## type: int
## preF: -k
## yml: 1
## min-intronlen:
## type: int
## preF: -min-intronlen
## yml: 30
## max-intronlen:
## type: int
## preF: -max-intronlen
## yml: 3000
## threads:
## type: int
## preF: -threads
## yml: 4
## U:
## type: File
## preF: -U
## yml: ./data/SRR446027_1.fastq.gz
## new_input1:
## type: File
## preF: -b1
## yml: myfile1
## new_input2:
## type: File
## preF: -b2
## yml: myfile2
## new_input3:
## type: File
## preF: -b3
## yml: myfile3
## *****Parsed raw command line*****
## hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz -b1 myfile1 -b2 myfile2 -b3 myfile3
cmdlist(cmd5)
## $defaultid
## $defaultid$hisat2
## [1] "hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz -b1 myfile1 -b2 myfile2 -b3 myfile3"
cmd6 <- appendParam(cmd, "inputs", index = 1:2, after=0, append = new_inputs)
## Replacing inputs
## *****Inputs*****
## new_input1:
## type: File
## preF: -b1
## yml: myfile1
## new_input2:
## type: File
## preF: -b2
## yml: myfile2
## new_input3:
## type: File
## preF: -b3
## yml: myfile3
## S:
## type: File
## preF: -S
## yml: ./results/M1A.sam
## x:
## type: File
## preF: -x
## yml: ./data/tair10.fasta
## k:
## type: int
## preF: -k
## yml: 1
## min-intronlen:
## type: int
## preF: -min-intronlen
## yml: 30
## max-intronlen:
## type: int
## preF: -max-intronlen
## yml: 3000
## threads:
## type: int
## preF: -threads
## yml: 4
## U:
## type: File
## preF: -U
## yml: ./data/SRR446027_1.fastq.gz
## *****Parsed raw command line*****
## hisat2 -b1 myfile1 -b2 myfile2 -b3 myfile3 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz
cmdlist(cmd6)
## $defaultid
## $defaultid$hisat2
## [1] "hisat2 -b1 myfile1 -b2 myfile2 -b3 myfile3 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz"
Editing output param
new_outs <- list(
"sam_out" = "<F: $(inputs.results_path)/test.sam>"
)
cmd7 <- replaceParam(cmd, "outputs", index = 1, replace = new_outs)
## Replacing outputs
## *****Outputs*****
## sam_out:
## type: File
## value: $(inputs.results_path)/test.sam
## *****Parsed raw command line*****
## hisat2 -S ./results/M1A.sam -x ./data/tair10.fasta -k 1 -min-intronlen 30 -max-intronlen 3000 -threads 4 -U ./data/SRR446027_1.fastq.gz
output(cmd7)
## $defaultid
## $defaultid$hisat2
## [1] "./results/test.sam"