sanger-pathogens/vr-codebase — pull request #61 by CraigPorter (2012-03-02 11:16:04+00:00)
Title: Import_iRODS_fastq validates compressed fastq against iRODS.

Solution to occasional problem where LSF would kill the bam to fastq conversion and the truncated files created by the killed job would affect the rescheduled job.
- The bam to fastq step was split into two stages, a translate bam to fastq step and a compress-and-validate step.
- The translation step deletes any files from failed jobs before restarting. The compress step overwrites any files from failed jobs.
- The validation against irods was moved from the update database step to the compress-and-validate step.
- A new fastqcheck file generated from the compressed fastq is checked against iRODS.