Implement MIPs alignment

[Nicklas Nordborg]

The next step after demux in the MIPs pipeline is an alignment step. A new wizard for starting this should be implemented. More details later...

[Nicklas Nordborg]

In 5826:

References #1218: Implement MIPs alignment

Started to implement this wizard. A GUI for selecting merged sequences has been created. Functionality for submitting a job to the cluster has been implemented, but the script will not do anything except copy the FASTQ files to the temporary working directory on the node.

[Nicklas Nordborg]

In 5827:

References #1218: Implement MIPs alignment

Added Trimmomatic steps to the script. Logging and error handling is not fully implemented yet.

[Nicklas Nordborg]

In 5828:

References #1218: Implement MIPs alignment

Added FastqToSam step that convertes paired FASTQ files to BAM format.

[Nicklas Nordborg]

In 5829:

References #1218: Implement MIPs alignment

Added AnnotateBamWithUmis step.

[Nicklas Nordborg]

In 5830:

References #1218: Implement MIPs alignment

Added alignement with novoalign and merging of BAM files to a single BAM.

[Nicklas Nordborg]

In 5831:

References #1218: Implement MIPs alignment

Final steps in the alignment pipeline. Re-headers, splitting and marking duplicates. All critical work has been done. There are still some collections of metrics to implement, as well as error handling and storing result files back to the project archive.

[Nicklas Nordborg]

In 5833:

References #1218: Implement MIPs alignment

Started to re-design the MIPs alignment script. Moved a lot of functionality into an external script (mips_functions.sh). The Trimmomatic script has been fixed including logging and error handling.

[Nicklas Nordborg]

In 5834:

References #1218: Implement MIPs alignment

Started to implement a script with helper functions for the MIPs alignment procedure.

[Nicklas Nordborg]

In 5835:

References #1218: Implement MIPs alignment

Re-designed the two steps that convert FASTQ files to BAM and annotate them with UMI information.

[Nicklas Nordborg]

In 5836:

References #1218: Implement MIPs alignment

Added functions for converting FASTQ to BAM and annotating with UMI information.

[Nicklas Nordborg]

In 5837:

References #1218: Implement MIPs alignment

Re-designed the alignment and merge step.

[Nicklas Nordborg]

In 5838:

References #1218: Implement MIPs alignment

Added functions for the novoalign and merge steps.

[Nicklas Nordborg]

In 5839:

References #1218: Implement MIPs alignment

Re-designed the post-processing steps: re-header, split and mark duplicates.

[Nicklas Nordborg]

In 5840:

References #1218: Implement MIPs alignment

Added functions for re-header, split and mark duplicates.

[Nicklas Nordborg]

In 5841:

References #1218: Implement MIPs alignment

Finalizing the MIPs alignment script by implementing the last two steps for collecting metrics. Results files are copied back to the project archive and linked in BASE to the alignment item.

Still need to implement importing some numbers as annotations from the metrics data.

[Nicklas Nordborg]

In 5842:

References #1218: Implement MIPs alignment

Added functions for collecting metrics.

[Nicklas Nordborg]

In 5843:

References #1218: Implement MIPs alignment

Importing some numbers from the metrics files to annotations. Existing annotations:

• ALIGNED_PAIRS
• READ_PAIRS_EXAMINED
• READ_PAIR_DUPLICATES
• FRACTION_DUPLICATION

New annotation:

• ALIGNED_BASES

[Nicklas Nordborg]

In 5844:

References #1218: Implement MIPs alignment

Adding JSP and javascript file that should have been included in [5826].

[Nicklas Nordborg]

In 5845:

References #1218: Implement MIPs alignment

Added manual confirmation wizard for MIPs alignment. It will display some information and allow registration of successful and failed alignments. Since we don't know what the next step is yet, nothing more is done.

Added auto-confirmation for the MIPs alignment. It will currently only clear the auto-confirm flag and the alignment will appear in the manual confirmation wizard.

[Nicklas Nordborg]

In 5846:

References #1218: Implement MIPs alignment

Fixed some comments.