renderReport.RdRender the technical report file to the specified output format using pandoc.
renderReport(sysargs, fileName ="SPR_Report",
rmd_title = "SPR workflow Template - Report",
rmd_author = "Author",
rmd_date= "Last update: `r format(Sys.time(), '%d %B, %Y')`",
type = c("html_document"),
desc = "This is a workflow template.",
quiet = FALSE, open_file = TRUE)object of class SYSargsList.
character string naming a file output. Default is "spr_report.Rmd".
string, title of the Rmd.
string, author(s) of the Rmd, put all authors in a single character string.
string, date header of Rmd.
The R Markdown output format to convert to. The option
can be the name of a format (e.g. "pdf_document" or "html_document").
string, or character vector of strings, some description text in format Rmarkdown that will be added to the document before the workflow steps start. It can be a single line or multiple lines by providing a character vector, each item is one line.
If set to TRUE, all messages returned by the function will be suppressed.
Default is TRUE.
It will return an SYSargsList updated, with the file path location.
See also as SYSargsList-class.
sal <- SPRproject(overwrite = TRUE)
#> Recreating directory '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject'
#> Creating file '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/SYSargsList.yml'
file_path <- system.file("extdata", "spr_simple_wf.Rmd", package = "systemPipeR")
sal <- importWF(sal, file_path = file_path, verbose = FALSE)
#> Now check if required tools are installed
#> Check if they are in path:
#> Checking path for gzip
#> PASS
#> Checking path for gunzip
#> PASS
#> step_name tool in_path
#> 1 gzip gzip TRUE
#> 2 gunzip gunzip TRUE
#> All required tools in PATH, skip module check. If you want to check modules use `listCmdModules`
targetspath <- system.file("extdata/cwl/example/targets_example.txt", package = "systemPipeR")
appendStep(sal) <- SYSargsList(step_name = "echo",
targets = targetspath, dir = TRUE,
wf_file = "example/workflow_example.cwl", input_file = "example/example.yml",
dir_path = system.file("extdata/cwl", package = "systemPipeR"),
inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_"))
sal <- renderReport(sal, open_file = FALSE)
#> Step name echo exist in SYSargsList but not in template.
#> It will be added as a new step in report, consider add it to your template first, and then use `sal <- importWF(sal, 'xx.Rmd', update = TRUE)` to update the template first before rendering report.
#>
#> Attaching package: ‘BiocStyle’
#> The following object is masked from ‘package:systemPipeR’:
#>
#> output
#>
#>
#> processing file: SPR_Report.Rmd
#>
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|.... | 7%
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|....... | 13% (setup)
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|........... | 20%
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|............... | 27% (load_library)
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|.................. | 33%
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|...................... | 40% (export_iris)
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|.......................... | 47%
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|............................. | 53% (gzip)
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|................................. | 60%
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|..................................... | 67% (gunzip)
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|........................................ | 73%
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|............................................ | 80% (stats)
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|................................................ | 87%
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|................................................... | 93% (echo)
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|.......................................................| 100%
#> output file: SPR_Report.knit.md
#> /usr/bin/pandoc +RTS -K512m -RTS SPR_Report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output SPR_Report.html --lua-filter /home/runner/work/_temp/Library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/runner/work/_temp/Library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --wrap preserve --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tmp/Rtmp7ygQ4c/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css /home/runner/work/_temp/Library/BiocStyle/resources/html/bioconductor.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp7ygQ4c/rmarkdown-str486d3653a4e.html --variable code_folding=show --variable code_menu=1
#>
#> Output created: SPR_Report.html
#> Success! Report created at SPR_Report.html