Closed ingkebil closed 5 years ago
As a member of TEAPOT, I want to be able to use fastq files from HiSeq X flowcells on Hasta, so I can analyze or reanalyze a case.
Problem: HiSeqX demultiplexing is now running on Rasta.
Suggested solution:
Partly solved here: https://github.com/Clinical-Genomics/demultiplexing/pull/74
Changes need to be made to demultiplexing scripts/hiseqx/xcheckfornewrun.bash, scripts/hiseqx/xdemuxtiles.bash, scripts/hiseqx/xdemuxtiles.batch
scripts/hiseqx/xcheckfornewrun.bash
scripts/hiseqx/xdemuxtiles.bash
scripts/hiseqx/xdemuxtiles.batch
[x] Have IT install same version of bcl2fastq that is installed on Rasta on Hasta
[x] scripts/hiseqx/xcheckfornewrun.bash
[x] scripts/hiseqx/xdemuxtiles.bash
[x] scripts/hiseqx/xdemuxtiles.batch
[ ] remove the copycomplete.txt trigger from deliver and possibly add another trigger?
[ ] activate the prod env in checkfornewdemuxonhasta.sh
checkfornewdemuxonhasta.sh
[ ] Create test specification
[ ] Validate
[ ] Add crontab entry: ... copy crontab entry with xcheckfornewrun.bash from rasta ...
... copy crontab entry with xcheckfornewrun.bash from rasta ...
@ingkebil Is this still happening in the background for non-complicated FCs? Or is the NAS access denied problem going to interfere with this?
This is not happening anymore.
As a member of TEAPOT, I want to be able to use fastq files from HiSeq X flowcells on Hasta, so I can analyze or reanalyze a case.
Problem: HiSeqX demultiplexing is now running on Rasta.
Suggested solution:
Partly solved here: https://github.com/Clinical-Genomics/demultiplexing/pull/74
Changes need to be made to demultiplexing
scripts/hiseqx/xcheckfornewrun.bash
,scripts/hiseqx/xdemuxtiles.bash
,scripts/hiseqx/xdemuxtiles.batch
[x] Have IT install same version of bcl2fastq that is installed on Rasta on Hasta
[x]
scripts/hiseqx/xcheckfornewrun.bash
[x]
scripts/hiseqx/xdemuxtiles.bash
[x]
scripts/hiseqx/xdemuxtiles.batch
Change params of bcl2fastq to match the ones suggested for NovaSeq (see Novaseq US)[ ] remove the copycomplete.txt trigger from deliver and possibly add another trigger?
[ ] activate the prod env in
checkfornewdemuxonhasta.sh
[ ] Create test specification
[ ] Validate
[ ] Add crontab entry:
... copy crontab entry with xcheckfornewrun.bash from rasta ...