GitLab

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.

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

Revert back to gmap 2014 12 23

See merge request !6

This tests the fix for #issue-11, which was resolved by a new upstream release
of the gmap aligner. The same upstream release also fixes #issue-12.

 - Upgrade pytest-workflow to version 1.4.0, which adds support for
   contains_regex.
 - Update test cases to match the values produced by the new version of gsnap.
   Use contains_regex to reduce the sensitivity of the test cases to small
   changes in values.
 - Change the MV4-11 FLT3 hotspot mutation test to a different variant. The
   previous variant was in a hard to map region, so it is unclear if it is an
   error when it could not be found.

To simplify the test, we compare the expression of the relevant MECOM
exon with the MECOM gene itself, and reduce the threshold to call
overexpression in the config file. This way, we do not have to add
additional read data to the repository.

This was requested by Hematology, since they use the amino acid
changes to determine the clinical relevance of a mutation.

Merge devel into master

See merge request !5

# Conflicts:
#   environment.yml
#   includes/fusion/Snakefile

Merge Gitlab ci into devel

Add gitlab-ci integration to HAMLET. The jobs run on the LUMC SLURM cluster.

See merge request !4

Also add the final pdf report as an artifact

In some rare cases, the fastqc rules would randomly crash when the JVM
could not allocate required space for the java temp folder. By explictly
setting fastqc to use /tmp as java temp folder, this bug is resolved.