GitLab

Fusioncatcher crashes if the maximum number of junction reads is
exceeded. This commit adds a parameter to the fusioncatcher rule to
make this configurable, and also increases the default limit from 100000
to 150000.

This fixes a crash in the generation of the pdf report when there is
expression of the MECOM gene. If there is MECOM expression, the read
counts are actually floats, not integers, which leads to a crash.

HAMLET has been developed using whole RNA sequencing. When it is used to
analyse targeted RNA-Seq data, various tools find no results, which can
lead to crashes in various parts of the pipeline.

The targeted RNA-Seq files were added were kindly provided by the
Radboudumc

Some tools crash when they receive empty input files (such as when 0
variants are found). The updated biocontainer images contain a newer
version of the crimson library to gracefully handle these cases.

Fusioncatcher crashes if the maximum number of junction reads is
exceeded. This commit adds a parameter to the fusioncatcher rule to
make this configurable, and also increases the default limit from 100000
to 150000.

Docker hub has started to remove unused images from free accounts, which
means that it might remove images used by this pipeline without notice.
Therefore the pipeline now exclusively uses images from quay.io or
official repositories from docker hub, which do not have this
limitation.

Fix #12 - SingularityCE version not recognised

See https://github.com/snakemake/snakemake/issues/991 for details.

- Rename a variable named 'count' since that has become a reserved
  keyword in Snakemake.
- Remove tests for an exact version of Snakemake.
- Add a Changelog file.

Enable testing via github workflows

This fixes a crash in the generation of the pdf report when there is
expression of the MECOM gene. If there is MECOM expression, the read
counts are actually floats, not integers, which leads to a crash.

Add explanation on how to run the pipeline and the importance of using
the --use-singularity flag.

Add an example on manually running one of the test cases.

Add an explanation on the different branches and how to use them.

Since external users cannot submit issues or pull requests without an
account for the LUMC gitlab instance, we should refer them to the public
github instance of HAMLET.

The pipeline graph doesn't add a lot of information, and it doesn't
render on github, so it was removed.

Use the tools library to determine file extension

See merge request !8

The previous code determined the extension by splitting the file path on a dot
(.), which failed when the file path contains dots in folder names.

This commit fixes issue #14

Merge development into master

See merge request !7