A Fastq file may contain an empty sequence after cutAdapter, Here A base N is set to an empty sequence with 0 base quality value". This tool takes fastq file as input and output, but also can read from stdin and writer to stdout, so it can insert into the pipe on our new WDL script.
Type of change
Please delete options that are not relevant.
[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update
How Has This Been Tested?
unit tests is added, tested on small real data. It will also run by new WDL
Are WDL Updates Required?
It is an independent new took, and not yet used by any current WDL pipeline. Any current WDL pipeline won't be affected. A new WDL script is created, which implements this tool after cutAdapter, and pass output fastq to BWA mapping, and also creates an uBAM (unmapped BAM). Thi new WDL script will be tested after its branch is merged into the master. This new WDL script named fasqTobam.wdl may replace the current mapPairedChunks.wdl.
Checklist:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
ChristinaXu2017
commented
2 years ago
Description
A Fastq file may contain an empty sequence after cutAdapter, Here A base N is set to an empty sequence with 0 base quality value". This tool takes fastq file as input and output, but also can read from stdin and writer to stdout, so it can insert into the pipe on our new WDL script.
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
unit tests is added, tested on small real data. It will also run by new WDL
Are WDL Updates Required?
It is an independent new took, and not yet used by any current WDL pipeline. Any current WDL pipeline won't be affected. A new WDL script is created, which implements this tool after cutAdapter, and pass output fastq to BWA mapping, and also creates an uBAM (unmapped BAM). Thi new WDL script will be tested after its branch is merged into the master. This new WDL script named fasqTobam.wdl may replace the current mapPairedChunks.wdl.
Checklist: