FastqPuri
Functions | Variables
Rcommand_Sreport.c File Reference

get Rscript command for Sreport More...

#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include "Rcommand_Sreport.h"
#include "init_Sreport.h"
#include "defines.h"
#include "config.h"
Include dependency graph for Rcommand_Sreport.c:

Functions

char * command_Sreport ()
 returns Rscript command that generates the summary report in html More...
 

Variables

Iparam_Sreport par_SR
 

Detailed Description

get Rscript command for Sreport

Author
Paula Perez paula.nosp@m.pere.nosp@m.zrubi.nosp@m.o@gm.nosp@m.ail.c.nosp@m.om
Date
09.08.2017

Function Documentation

◆ command_Sreport()

char* command_Sreport ( )

returns Rscript command that generates the summary report in html

# To run between quotation marks after: Rscript_RBioC -e (Rscript)
inputfolder = normalizePath( <par.SR.inputfolder>, mustWork = TRUE);
output = <par_SR.outputfile>;
output_file = gsub('.* /', '', output);
path = gsub('[^/]+$', '', output);
if (path != '') {
outputfile = paste0(normalizePath(path, mustWork = TRUE), '/', outputfile);
} else {
outputfile = paste0(cwd, '/', output_file); # cwd: current working dir
};
rmarkdown::render(<par_SR.Rmd_file>,
params = list(inputfolder = inputfolder, version= VERSION),
output_file = output_file)

Variable Documentation

◆ par_SR

input parameters Sreport