Describe the bug
Some paired-end fastq files (mainly from the sequencing facility, not SRA) contain a - in their seqID's (probably in the flowcell description part), and they don't match the regex for Casava >=1.8 format, e.g. @M02861:265:000000000-DMNF3:1:1101:12765:1724 1:N:0:GCGTCAAT; as a result, the samples don't get recognized as pairs leading to incorrect library type and read orientation inference.
Expected behavior
Update the regex as these seqID's should match the Casava format.
Describe the bug Some paired-end fastq files (mainly from the sequencing facility, not SRA) contain a
-in their seqID's (probably in the flowcell description part), and they don't match the regex for Casava >=1.8 format, e.g.@M02861:265:000000000-DMNF3:1:1101:12765:1724 1:N:0:GCGTCAAT; as a result, the samples don't get recognized as pairs leading to incorrect library type and read orientation inference.Expected behavior Update the regex as these seqID's should match the Casava format.