Create MIPs flow cell and start/end/confirm sequencing

[Nicklas Nordborg]

We need at least one wizard for registering that sequencing has started for a MIPs pool. Depending on the complexity we may divide this to a "Create flow cell" wizard, a "Lab protocol" wizard, a "Clustering" wizard and a "Sequencing started" wizard.

[Nicklas Nordborg]

In 5439:

References #1142: Create MIPs flow cell and start sequencing

Added a "Create flow cell" wizard. This is very similar to the same wizard in the "RNAseq" pipeline, but have different default selection (HiSeq with a 2-lane flow cell) and doesn't track used quantity.

[Nicklas Nordborg]

In 5441:

References #1142: Create MIPs flow cell and start sequencing

Added Pipeline=RNAseq filter to only count/display the correct flow cells in the RNA sequencing wizards.

Added counter for MIPs flow cells.

[Nicklas Nordborg]

In 5453:

References #1142: Create MIPs flow cell and start sequencing

Added more presets with different settings for number of reads.

Added a second "Index" field.

[Nicklas Nordborg]

In 5462:

References #1142: Create MIPs flow cell and start sequencing

Implemented the "Lab protocol for sequencing" wizard in the MIPs pipeline. Only minor changes compared to the RNAseq pipeline.

[Nicklas Nordborg]

In 5463:

References #1142: Create MIPs flow cell and start sequencing

Remove debug code.

[Nicklas Nordborg]

In 5469:

References #1142: Create MIPs flow cell and start sequencing

Added the FlowCellType annotation to Hardware items with Sequencer subtype.

This is used for filtering which sequencers that are available for selection in the "Register sequencing started" wizard. Existing sequencer hardware items should be updated or they will not appear in the selection list at all.

[Nicklas Nordborg]

In 5470:

References #1142: Create MIPs flow cell and start sequencing

Implemented the "Register sequencing started" wizard for the MIPs pipeline. It turned out that almost no changes were needed so the same wizard is shared between the two pipelines.

Auto-analyze probably doesn't work for the MIPs pipeline yet for a couple of reaseons:

• No HiSeq support for checking status of the sequencing
• The NextSeq check only supports a single index read

[Nicklas Nordborg]

In 5471:

References #1142: Create MIPs flow cell and start sequencing

Manual registration of sequencing run ended should now work also for HiSeq sequencing.

[Nicklas Nordborg]

In 5472:

References #1142: Create MIPs flow cell and start sequencing

Counters for the start page should now count the correct number of active sequencing runs.

[Nicklas Nordborg]

In 5474:

References #1142: Create MIPs flow cell and start sequencing

Added a pipeline script hiseq_status.sh. It is a script that is similar to the nextseq_status.sh script and is used to get information about an ongoing HiSeq sequencing run. It is believed to give us all the information that is needed to monitor the progress and to enable us to detect whan the sequencing has ended.

We need some more counters to get a values that we can compare to the number of BCL files:

LaneCount * SurfaceCount * SwathCount * TileCount * (total reads) == BclCount

The nextseq_status.sh script has also been updated to give us the Index2Read value.

[Nicklas Nordborg]

In 5475:

References #1142: Create MIPs flow cell and start sequencing

The "Auto-analyze" option should now work for HiSeq. It has not been tested fully. If it works it will most likely try to start a RNAseq demux so it will probably fail soon after that.

[Nicklas Nordborg]

In 5476:

References #1142: Create MIPs flow cell and start sequencing

Updated the hiseq_status.sh script so that will check if a file or folder exists before trying to use it.

[Nicklas Nordborg]

In 5477:

References #1142: Create MIPs flow cell and start/end/confirm sequencing

Sequencing ended can now be detected also for HiSeq sequencing, but the picard step for checking data files will fail since the read-string is not generated correctly when there are four groups in the sequencing-cycles (read1-index1-index2-read2).

[Nicklas Nordborg]

In 5478:

References #1142: Create MIPs flow cell and start/end/confirm sequencing

The manual "confirm sequencing" wizard has been updated to work with both MIPs and RNAseq pipeline (controlled via a parameter). The "Check data files" functionality has also been updated and it should now work with HiSeq (actually, it did work before, the only problem was that a proper read-string could not be generated)

Auto-confirmation should now work for HiSeq/MIPs sequencing. No big changes here, but just a stop so that sequencing runs belonging to the MIPs pipeline are not started with the existing demux script.

[Nicklas Nordborg]

In 5484:

References #1142: Create MIPs flow cell and start/end/confirm sequencing

The sequencing started and ended wizard should also work for the MIPS_LIBRARY_PREP role.

[Nicklas Nordborg]

In 5485:

References #1146 and #1142. Added role MIPsSecondayAnalysis.

[Nicklas Nordborg]

In 5488:

References #1142: Create MIPs flow cell and start/end/confirm sequencing

Moved the "Confirm sequencing" wizard to the "sequencing" subfolder. Pipeline information is now submitted in the query string part of the URL so we can use that information to check for the correct permission when finishing registration.

[Nicklas Nordborg]

In 5491:

References #1146 and #1142.

Auto-confirmation of a MIPs sequencing run should now be able to start the correct demux job.

[Nicklas Nordborg]

In 5526:

References #1130, #1135, #1142, #1146. Fixing and getting rid of some 'TODO' entries in the code.

[Nicklas Nordborg]

In 5582:

References #1146 and #1142. Changed the MIPsSecondaryAnalysis role to a group. This should make it behave similar to the SecondaryAnalysis group that is used for RNAseq.