comparison bamqc_wrapper.pl @ 4:3d690162d629 draft

Added more details for the required dependencies.

3:9537dd9dd18b

my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1); 
mkdir "$tempdir", 077 unless -d "$tempdir";
INFO "\nTemporary directory:\n$tempdir";


# ---------------------- Output files ---------------------------------#
########################################################################
# Two possible scenarios
# - output is written to the file at the output location in config file
# - output is moved to the output file location

# open (SAMOUTPUT, ">$para{'output_sam'}") 
# 	or ( ERROR "Could not open output file for writing! (file:$para{'output_sam'}" and die );
# print SAMOUTPUT "Here comes sam\n";
# close (SAMOUTPUT);	


# -------------------- Assembling command  ----------------------------#
########################################################################
my $outdir="bamqc_output";
my $qualimap_path="";						# for tool_dependency later on
my $command = $qualimap_path."qualimap bamqc --outdir $outdir"; # this will ultimately be executed

4:3d690162d629

my $tempdir = File::Temp->tempdir('tmpXXXXX', DIR => $galtemp, CLEANUP => 1); 
mkdir "$tempdir", 077 unless -d "$tempdir";
INFO "\nTemporary directory:\n$tempdir";

# -------------------- Assembling command  ----------------------------#
########################################################################
my $outdir="bamqc_output";
my $qualimap_path="";						# for tool_dependency later on
my $command = $qualimap_path."qualimap bamqc --outdir $outdir"; # this will ultimately be executed