cg transfer flowcell correctly adds undetermined fastq files for HiseqX samples to housekeeper

[emiliaol]

As a member of team bioinfo prod I want all the fastq files to be available for analysis for old hiseq X samples so that I don't have to rerun analysis based on missing indata

Problem: cg transfer flowcell HMNVTCCXYshould also link the undetermined fastq files for all samples to housekeeper, but it now only adds the regular files.

Steps to reproduce

1. on hasta up
2. cg transfer flowcell HMNVTCCXY
3. housekeeper get ACC4667A1

The list of files is now:

Expected outcome / suggested solution: The list of files should also contain 4 additional fastq files with the word Undetermined in the name:

HMNVTCCXY-l2t11_Undetermined_S0_L001_R1_001.fastq.gz 
HMNVTCCXY-l2t11_Undetermined_S0_L001_R2_001.fastq.gz 
HMNVTCCXY-l2t21_Undetermined_S0_L001_R1_001.fastq.gz
HMNVTCCXY-l2t21_Undetermined_S0_L001_R2_001.fastq.gz  

This should ofc only happen if there is a single sample in the lane, so pooled samples should not have the undetermined file linked.

Questions: Q: Is this a problem for all HiSeq X flow cells? A: I don't know.

What needs to be done on the planning meeting:

• Estimate storypoints
• Remember to add label PBL Teamname

See https://github.com/Clinical-Genomics/development/blob/master/git/issue-reports.md for more!

[Mropat]

@henrikstranneheim @barrystokman @moahaegglund @karlnyr Is this related to the recent Undetermined file discussion? Can this be closed?

[moahaegglund]

Yes, this is connected, don't close it.

[karlnyr]

@moahaegglund This issue is resolved right? With this PR

[moahaegglund]

@moahaegglund This issue is resolved right? With this PR

Undetermined fastq files are linked correctly to the folders under Unaligned thanks to that PR but they are not included in Housekeeper, right? I think it's like that and if that's the case this issue is not resolved yet.

[karlnyr]

Ok great, I will look into that then!

[henrikstranneheim]

This has been resoled!