dynamic is a special keyword in Snakemake that can be used to mark
outputs when the number of output files is not known before execution.
This is the case when using scatterregions, since the number of outputs
depends on the size of the reference genome and the size of the
scattered chunks.

See
https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#dynamic-files
for details

This fixes a rare bug where picard runs out of disk space on when spilling
reads to disk, because it uses the internal java temp dir as a location. This
closes issue #42

Deprecate conda, make pipeline more general

See merge request !13

# Conflicts:
#   Snakefile

When a repository changes its Suite value from 'testing' to 'stable',
this change needs to be accepted or the repository will not be used.
This leads to errors in the gitlab-ci testing since the latest version
of pip3 is not installed.

For some reason, pip fails in the python3.6 container on install
python>=3.5. This makes all gitlab-ci tests fail.

Fix typo in resource requirement.

See merge request !12

Hutspot sometimes fails on the fastqc analysis due to Java heap space
memory errors. It is not possible to set the memory usage by fastqc
directly, since this is done by the perl wrapper script. However, the
amount of memory that is set by the wrapper scales with the number of
threads that fastqc uses. Therefore, the number of threads was
increased, effectively increasing the memory fastqc can use.

The wc which is present in the biocontainers has a maximum integer size
of just 2^32, which means the counter resets every 4 billion bases. This
commit adds a custom python script to solve issue #39.

While the python tool is slower than wc, it has the advantage that we
only have to parse the bam file once, since it can count both the lines
and the number of bases in one go. That should save a bit on the time.

This commit also updates samtools from version 1.6 to 1.7.

There were some failed tests due to changes in the order of checks in
the Snakefile, which caused the wrong error to be thrown when there were
multiple missing files. This commit fixes that issue.

The KNOWN_SITES argument has been made mandatory for now, and this
requirement has also been added to the test cases.

Remove deprecated sanity checks for the GAKT jar file and the different
VCF files that are used for BQSR.
Remove the 'functional' tag since it was identical to integration.
Remove the conda specific test cases, since conda has been deprecated.

Fix picard heapspace error in align rule

See merge request !11

In the Singularity image for picard, the default heapsize is too small,
leading to crashes in the pipeline when the rule 'align' runs out of
heap space. The solution is to explicitly specify the heap space that
picard can use, thereby overriding the default value that is set in the
Singularity image.

This issue was reported on capture-lumc-wrapper, see
https://git.lumc.nl/klinische-genetica/capture-lumc/capture-lumc-wrapper/issues/26
for details.

Bcftools concat in stead of GATK catvariants