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.

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[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:

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 [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.