fix 2500 sample sheet issues

[barrystokman]

This PR adds conversion of old 2500 sample sheets so demuxing and cgstats works on Hasta.

How to prepare for test:

• [x] ssh to hasta
• [x] install on stage: bash servers/resources/hasta.scilifelab.se/update-demux-stage.sh [THIS-BRANCH-NAME]

How to test:

• [x] rsync -av /home/proj/production/flowcells/2500/runs/140818_D00410_0089_AH9M8MADXX /home/proj/stage/flowcells/2500/runs/
• [x] make sure all run dirs in /home/proj/stage/flowcells/2500/runs/ have a demuxstarted.txt EXCEPT 140818_D00410_0089_AH9M8MADXX
• [x] run bash /home/proj/stage/bin/git/demultiplexing/scripts/2500/stage/checkfornewrun.bash /home/proj/stage/flowcells/2500/runs/ /home/proj/stage/demultiplexed-runs/ &>> /home/proj/stage/logs/checkfornewrun.2500.log

Expected test outcome:

• [x] check that demultiplexing has finished and started correctly
• [x] check /home/proj/stage/logs/checkfornewrun.2500.log and /home/proj/stage/demultiplexed-runs/140818_D00410_0089_AH9M8MADXX/projectlog.*.log for errors and inconsistencies
• [ ] Take a screenshot and attach or copy/paste the output.

Review:

• [ ] code approved by
• [x] tests executed by @barrystokman
• [ ] "Merge and deploy" approved by Thanks for filling in who performed the code review and the test!

This version is a:

• [x] PATCH - when you make backwards compatible bug fixes or documentation/instructions

[barrystokman]

[barrystokman]

Only undetermined fastqs:

[barrystokman]

demux sheet convert /home/proj/stage/flowcells/2500/runs/140818_D00410_0089_AH9M8MADXX/SampleSheet.csv:

Preconditions cgstats select H9M8MADXX:

Post demux cgstats select H9M8MADXX:

Comparison post demux cgstats select H9M8MADXX in P_main:

[barrystokman]

Bumped: