Automatic demultiplexing of iseq runs

[patrikgrenfeldt]

This PR adds demuliplexing support for iSeq

How to setup:

1. install on stage of thalamus: bash servers/resources/clinical-preproc.scilifelab.se/update-demux-stage.sh Automatic-demultiplexing-of-iSeq-runs
2. cd cd /home/hiseq.clinical/SCRIPTS/git/demultiplexing/
3. git pull
4. git checkout Automatic-demultiplexing-of-iSeq-runs
5. activate stage: source activate stage
6. cd /home/hiseq.clinical/SCRIPTS/git/demultiplexing/scripts/iseq/

How to test demultiplexing:

1. run following command: bash demux-iseq.bash /home/hiseq.clinical/iseq/runs/20190528_FS10000534_7_BPC29611-3324/ /home/hiseq.clinical/iseq/demux/

Expected outcome:

• [x] demultiplexing should start happily

How to test checking for new run:

1. run following command: bash checkfornewrun.bash /home/hiseq.clinical/iseq/runs/ /home/hiseq.clinical/iseq/demux/

Expected outcome:

• [x] all runs without a demuxstarted.txt file should start. All other should be mentioned as already demultiplexed.

Take a screenshot and attach or copy/paste the output.

Review:

• [x] code approved by @ingkebil @barrystokman
• [x] tests executed by @patrikgrenfeldt @emiliaol tested in cgstats iseq PR
• [x] "Merge and deploy" approved by @ingkebil Thanks for filling in who performed the code review and the test!

This is |minor| version bump because we add func without altering the old one

[patrikgrenfeldt]

Test result:

👎

[patrikgrenfeldt]

Test result demux:

👍

👎

[patrikgrenfeldt]

Test result check for new demux:

👍

[ingkebil]

put both files through a linter :)

[ingkebil]

Code looks good! Feel free to approve in my name when tests are completed and the version bump is motivated

[ingkebil]

Approving M&D :rocket:

[ingkebil]

Just wondering as this is also renaming the fastq files, did you check if the fastq filenames were sane?

[patrikgrenfeldt]

Just wondering as this is also renaming the fastq files, did you check if the fastq filenames were sane?

No we did not. What should the names be? How do we know they are correct?

[ingkebil]

@emiliaol are we even using the fastq files for something afterwards or are we only demuxing to get the statistics? If the latter, we can drop the fastq renaming code.

[ingkebil]

eeh, let's just leave the code in for now. I'm unsure if cgstats is using the restructured dir or not.

[ingkebil]

deployed