Add test to make sure the markdup and baserecal groups receive the
correct inputs when a sample has multiple readgroups.

The directory output for the fastqc tasks is causing issues on the
shared file system of the cluster, since it cannot properly determine
the age of the folder. As a result, it re-runs the fastqc tasks every
time a workflow is restarted, regardless of whether the task has already
completed.

To prevent this, a single dummy output file '.done' has been added to
the fastqc tasks which will be written when fastqc exits successfully.

The base recalibration (BQSR) step of the pipeline can take up to 7 hours for
WGS samples, which is a significant part of the total run time.

The developers of GATK state that BQSR requires at least 100M bases per read
group: "We usually expect to see more than 100M bases per read group; as a rule
of thumb, larger numbers will work better."

A human WGS sample with an average read depth of 43x has almost 1300 times that
amount of bases. The analysis of these samples would be sped up greatly by
restricting BQSR to a single chromosome.

The base recalibration step of the pipeline can take up to 7 hours for
WGS samples, which is a significant part of the total run time.

The developers of GATK state that BQSR requires at least 100M bases per
read group: "We usually expect to see more than 100M bases per read
group; as a rule of thumb, larger numbers will work better."

A human WGS sample with an average read depth of 43x has almost 1300
times that amount of bases. The analysis of these samples would be sped
up greatly by restricting BQSR to a single chromosome.

Use 8 cores instead of just 1, according to the documentation speed
should almost scale linear with the cores provided.

Also reduce the compression level on the output file, since most time
for cutadapt is spent re-compressing the data after trimming the
adapters.

Revert "Remove explicit tmp folder"

See merge request !17

This reverts commit 1b7d807f

This should no longer be needed on the slurm cluster, where each task
can request the amount of tmp space it requires explicitly.

Removing the tmp from the shared filesystem back onto the host running
the analysis should also improve the performance of the pipeline.

This way, the same version of picard is used in all tasks in the
pipeline. This fixes issue #38

Add optional bed coverage output files

See merge request !16