GitLab

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

Unfortunately, this adds a limitation on the sample names that can be
used with Hutspot, since the naming of the samples in the multiQC parsed
output of picard MarkDuplicates is partly ambiguous.

This limitation has been added to the readme, and a check has been added
to the pipeline snakefile to throw an error when overlapping sample
names are detected.

Previously, Hutspot supported multiple bed files to calculate coverage
against. Because of this, the stats.json file had a nested structured
where the coverage based on each bed file was stored, including the name
of the bed file and the gender, according to that bed file.

Since the current version of Hutspot only supports a single bed file,
this structure has been simplified. All coverage statistics are now
directly under 'coverage' for each sample, and the 'gender' has been
moved out of the 'coverage' statistics to the sample level.

Hutspot now supports two bed files to calculate coverage. One is the
`targetsfile`, which was called `bedfile` before, and holds the targets
of the capture kit. The other one is `baitsfile`, which holds the bait
locations of the capture kit.

It is possible to specify only the `targetsfile`, but if you specify the
`baitsfile`, the `targetsfile` must be specified as well, since both are
required by picard HsMetrics.

Also added a test for invalid configuration files, and shortened the
jsonschema validation error to only show the human readable message.