Config file¶
Synopsis¶
-
[meta]
¶ Lists all the meta-data of current workflow.
Consist of the following options:
-
dataset.ID
¶ The name for the dataset, which will be the value of
${DatasetID}
Limit: a string (1) consist of
numbers
,alphabets
or'_'
(2) shorter than 20 characters
-
species
¶ The name of species, written to the QCreport and log
Limit: a string (1) consist of
numbers
,alphabets
or'_'
(2) shorter than 20 characters
-
assembly
¶ The assembly version, written to the QCreport and log
Limit: a string (1) consist of
numbers
,alphabets
(2) shorter than 10 characters
-
treatment
¶ The paths of treatment files
Limit: absolute or relative
path
of files in supported formats
-
control
¶ The paths of treatment files
Limit: absolute or relative
path
of files in supported formats
-
-
[ext]
¶ The external data and external tools to use. Read External Data and External Tools for a full explanation.
-
[steps]
¶ meta
Simpest config¶
Here is one of the simpest Cpipe workflow you can make.
1 2 3 4 5 6 7 8 9 | [meta]
dataset.ID = mydata_ctcf
species = human
assembly = hg19
treatment = .../GSM489301.fastq
[ext]
directory = .../Cpipe/data
|
Use your own path of Raw Data to replace the Line 6. And use the path of the directory used to store External Data to replace Line 9.
When saved to hello_cpipe.conf
, this config file can construct a powerful pipeline via:
$ Cpipe hello_cpipe.conf
When it finished about 2 hours later, you will get Processed Data and a Final PDF Report.
Examples about replicates¶
For example, there are five raw files. Three of them are replicates for treatment
and two of two for control
.
The file names may look like:
demo_treat1.fastq
demo_treat2.fastq
demo_treat3.fastq
demo_control1.fastq
demo_control2.fastq
Then you can write the [meta]
section like this:
1 2 3 4 5 6 7 8 9 | [meta]
dataset.ID = demo_replicate
# species = human
# assembly = hg19
treatment.1 = demo_treat1.fastq
treatment.2 = demo_treat2.fastq
treatment.3 = demo_treat3.fastq
control.1 = demo_control1.fastq
control.2 = demo_control2.fastq
|
Replace the commented in Line 2, Line 3 and Line 4 and complete other sections. Then load it with Cpipe.
For the notation of output files, the ${DatasetID}
will be demo_replicate
. The ${treat_rep}
will be 1
, 2
and 3
. The ${control_rep}
will be 1
and 2
.