Updates the QC pipeline in qc/pipeline to add a verification task which checks the integrity of Fastq files (i.e. can they be opened and read).
This PR is intended to address issue #854, although it should work for both compressed and uncompressed Fastqs.
The verification adds some overhead (as QC metrics are not generated until the Fastqs have been checked). Therefore, while it is always turned on in the standalone QC utility run_qc.py (where Fastqs can potentially come from any source) it is turned off in the auto_process.py run_qc command (which typically is executed on Fastqs directly from bcl2fastq or similar).
Updates the QC pipeline in
qc/pipelineto add a verification task which checks the integrity of Fastq files (i.e. can they be opened and read).This PR is intended to address issue #854, although it should work for both compressed and uncompressed Fastqs.
The verification adds some overhead (as QC metrics are not generated until the Fastqs have been checked). Therefore, while it is always turned on in the standalone QC utility
run_qc.py(where Fastqs can potentially come from any source) it is turned off in theauto_process.py run_qccommand (which typically is executed on Fastqs directly frombcl2fastqor similar).