RenameCHGenomicsFilename

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1. Decription

RenameCHGenomicsFilename is designed for rename fastq.gz files generated by CloudHealth Genomics.

The rules of fastq.gz files : [runID]_[machineId][flowcellID]_[CHGID]-[LibName]-[SampleName]-[Barcode]_[LaneId]_[ReadNum].fastq.gz

It looks like this: S0001_01A_CHG000000-LIBNAME-SAMPLENAME-CCGGTTAA_L008_R2.fastq.gz

Some custumors do not want to get the fastq file in this style names. Some donot want the CHGID appears in the names, or LibName,SampleName,Barcode,LaneId.

So RenameCHGenomicsFilename is created.RenameCHGenomicsFilename is a golang based app.

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2. Usage

RenameCHGenomicsFilename can be run in both windows/linux OS, or anyother platforms which golang support. Help Information for RenameCHGenomicsFilename:

RenameCHGenomicsFilename
A fastq.gz renamer from Cloudhealth Genomics, avaliable command : 
        (1)rename;
        (2)rebuilddir;
Please use help for details

Author: Qinghui Li
Email: liqh@cloudhealth99.com
Company: CloudHealth Genomics

Usage:
  RenameCHGenomicsFilename [flags]
  RenameCHGenomicsFilename [command]

Available Commands:
  help        Help about any command
  rebuild     re-build the structure of the delivering fastq files
  rename      rename is used for rename fastq file(s) to user specified stype
  version     Print the version number of RenameCHGenomicsFilename

Flags:
  -h, --help   help for RenameCHGenomicsFilename

Use "RenameCHGenomicsFilename [command] --help" for more information about a command.
```language

NOTICE: all the command can by in short or long parameters,like -h or --help.

2.1 rename module

Help information for rename module,by typing RenameCHGenomicsFilename rename -h

rename is used for rename fastq file(s) to user specified stype, avaliable Parameters: 
        (1)-marker :the region you want to remove from the samplenames[default:"4"]
                0: remove RunId,flowcellID,CHGID
                1: remove CHGID
                2: remove LibName
                3: remove SampleName
                4: remove Barcode
                5: remove LaneId
                12: remove CHGID & LibName
                14: remove CHGID & Barcode
                124: remove CHGID & LibName & Barcode
        (2)-dir :directory of the fastq files. eg: /online/projects/C150001-P001 [default:"./",means current dir,for linux OS]
        Any problem please contact  Qinghui Li  via liqh@cloudhealth99.com

Usage:
  RenameCHGenomicsFilename rename [flags]

Flags:
  -d, --dir string   specify a (relative/abs) path to fastq files (default "./")
  -h, --help         help for rename
  -m, --marker int   specify a marker to remove from filename[0/1/2/3/4/5/12/14/124]:chg id/original lib name/original samplename/barcode/lane id/CHGID & LibName/CHGID & Barcode/CHGID & LibName & Barcode (default 4)

2.2 rebuild module

Help information for rename module,by typing RenameCHGenomicsFilename rebuild -h

re-build the structure of the delivering fastq files，including fq files,md5 files, dir name, et.al.

Usage:
  RenameCHGenomicsFilename rebuild [flags]

Flags:
  -c, --customerid string   customer id , determined the style of fastq files structure. 
                Please input the correct customerid, like: C150001,C150003
  -d, --dir string          specify a (relative/abs) path to projectdir,like C150003-P999
  -h, --help                help for rebuild
  -p, --projectid string    projectid of the current delieverying (default "all")

3. Download

git clone https://github.com/snailQH/RenameCHGenomicsFilename.git
cd RenameCHGenomicsFilename
chmod 777 RenameCHGenomicsFilename

4. What's New

• 20170920 update the program with a new CLI cobra and update a new function rebuild ,which aims to rebuild the structure of fastq files into the style defined by custumers-self.

5. How ro run

1. run the app from source code:

You need to install golang before run from the source code.

go run main.go rename -d /online/projects/C170001-P001 -m 5 #remove the LaneId from filename[/online/projects/C170001-P001]

2. run the app in linux os:

rename:

./RenameCHGenomicsFilename rename -d /online/projects/C170001-P001 -m 5 //remove the LaneId from filename[/online/projects/C170001-P001]

rebuild:

./RenameCHGenomicsFilename rebuild -d /online/projects/C170001-P001 -p C170001-P001 -c C170001 //rebuild all the fastq files according to the style provided by customer C170001

3. run the app in windows os:

RenameCHGenomicsFilename.exe rename -d D:\\C170001-P001 -m 5 //remove the LaneId from filename[D:\\C170001-P001]

Warning: Run the RenameCHGenomicsFilename rename can rename all the *fastq.gz files who have he same name pattern with the CHG *fastq.gz files which may affect the irrelevant files.