Updates to correctly handle sets of single-ended SRA Fastq files in the QC pipeline, which don't have explicit read numbers in the Fastq names compared to paired-end SRA Fastqs (e.g. single-end version SRR123456.fastq.gz versus paired-end R1 version SRR123456_1.fastq.gz).
The lack of an explicit read number meant that the AnalysisFastq class (in the analysis module) returned the read number as None, causing issues in QC pipeline tasks where Fastqs would be filtered out unless their read number matched one of those assigned in the QC protocol (for example, the GetBamFiles task).
An update to the AnalysisFastq class now sets the read number to 1 rather than None for single-ended SRA Fastqs, and sets a new flag implicit_read_number to indicate that this has been assumed.
The update includes a pair of unit tests for the QC pipeline to check that both single and paired-ended SRA Fastqs are now handled correctly.
Updates to correctly handle sets of single-ended SRA Fastq files in the QC pipeline, which don't have explicit read numbers in the Fastq names compared to paired-end SRA Fastqs (e.g. single-end version
SRR123456.fastq.gzversus paired-end R1 versionSRR123456_1.fastq.gz).The lack of an explicit read number meant that the
AnalysisFastqclass (in theanalysismodule) returned the read number asNone, causing issues in QC pipeline tasks where Fastqs would be filtered out unless their read number matched one of those assigned in the QC protocol (for example, theGetBamFilestask).An update to the
AnalysisFastqclass now sets the read number to1rather thanNonefor single-ended SRA Fastqs, and sets a new flagimplicit_read_numberto indicate that this has been assumed.The update includes a pair of unit tests for the QC pipeline to check that both single and paired-ended SRA Fastqs are now handled correctly.