v1.1.0

Changes:

• Add an optional step to get metrics from the BAM file using Picard's CollectMultipleMetrics
• Add to the default config the cleanup of the work folder to avoid storing all intermediate BAM files after execution
• Add another optional step to run Picard's CollectHsMetrics, optionally with per target and per base coverage

v1.0.1

Changes:

• Use local temporary folders

v1.0.0

Changes:

• Migrate to conda environment
• Added tests + automate tests in gitlab
• Improved some skipping steps
• Chain several Picard commands so less intermdediate IO is happening
• Avoid using samtools at all, using Picard from within GATK4
• Added some extra files to output

v0.1.1

Minor changes

• When some steps are skipped the output BAMs are not links anymore
• The txt file with results points to the right paths

v0.1.0

First release