Include mutation signature analysis in the variant calling pipeline

[Nicklas Nordborg]

A mutation signature can be calculated from the filtered variants VCF. See ​https://cancer.sanger.ac.uk/cosmic/signatures_v2

The calculations are done with an R script and generate PDF plot and a text file with a score for each of 30 signature patterns.

The R script should be included in the variant call script and the pdf and text file should be stored and attached to the rawbioassay item together with the existing VCF files. The scores should be imported to annotations: MutationSignature1, ... MutationSignature30.

[Nicklas Nordborg]

In 5792:

References #1215: Include mutation signature analysis in the variant calling pipeline

Adding annotation types MutationSignature1, ..., MutationSignature30 to the installation wizard.

[Nicklas Nordborg]

In 5793:

References #1215: Include mutation signature analysis in the variant calling pipeline

0-pad names so that we get MutationSignature01 instead. It is nicer to have the annotations sorted in the expected order.

[Nicklas Nordborg]

In 5794:

References #1215: Include mutation signature analysis in the variant calling pipeline

Implemented support for parsing the output file with scores for the mutation signatures.

[Nicklas Nordborg]

In 5795:

References #1215: Include mutation signature analysis in the variant calling pipeline

Implemented a step in the variant calling pipeline for calling the mutation_signature.R script.

[Nicklas Nordborg]

In 5796:

References #1215: Include mutation signature analysis in the variant calling pipeline

Adding pipeline script for analyzing COSMIC mutation signature.

[Nicklas Nordborg]

In 5807:

References #1215: Include mutation signature analysis in the variant calling pipeline

Added a wrapper shell script for starting R scripts with R 3.6.2. We need to set PATH and LD_LIBRARY_PATH so that R can find the correct versions.

[Nicklas Nordborg]

In 5809:

References #1215: Include mutation signature analysis in the variant calling pipeline

Use the wrapper script to start the mutation signature R script.