fastqcCheck.txt

[Run]
working_dir = %(output_dir)s     
date = 030315
version = 1

[Step_1]
enable = True
Type = cmd
name = run quality check
description = run quality check
program = fastqc
parameters = -q --extract -o %(output_dir)s %(sra_dir)s/%(file_name)s.fastq
next_step = Step_3
error_step = Step_-1

[Step_2]
enable = False
Type = cmd
name = run quality check
description = run quality check
program = fastqc
parameters = -q --extract -o %(output_dir)s %(sra_dir)s/%(file_name)s.2.fastq
next_step = Step_3
error_step = Step_-1

[Step_3]
enable = True
Type = cmd
name = check quality summary 1
description = check quality summary
program = perl516 /home/alu/ilanas/Scripts/perl/check_fastqc_output.pl
parameters = %(output_dir)s/%(file_name)s.fastqc/summary.txt
next_step = Step_5
error_step = Step_-1

[Step_4]
enable = False
Type = cmd
name = check quality summary 2
description = check quality summary
program = perl516 /home/alu/ilanas/Scripts/perl/check_fastqc_output.pl
parameters = %(output_dir)s/%(file_name)s_2.fastqc/summary.txt
next_step = Step_5
error_step = Step_-1

[Step_-1]
Enable = True
Type = mail
name = error stage
description = error stage
program = mail
text=run of  %(output_dir)s ended with error
from=fulther@localhost
to=ronif10@gmail.com
parameters = -O %(output_dir)s/ "%(sra_dir)s"%(file_name)s.sra
next_step=Step_-2
error_step = Step_-2

[DEFAULT]
output_dir = /private7/common/Data/DataSets/beta_cells/fastqc/data1
sra_dir = /private7/common/Data/DataSets/beta_cells/fastq/data1
sam_file_name = sam