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.
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
.
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)
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")
git clone https://github.com/snailQH/RenameCHGenomicsFilename.git
cd RenameCHGenomicsFilename
chmod 777 RenameCHGenomicsFilename
- 20170920 update the program with a new CLI
cobra
and update a new functionrebuild
,which aims to rebuild the structure of fastq files into the style defined by custumers-self.
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]
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
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.