Release v1.7.2

Bugifix

Picard's CollectMultipleMetrics has an unmet dependency to R in the bioconda module. This is explicitly added here now.

Release v1.7.1

Bugfix

• BAMs with a header missing the SM tag in the read group header were failing. This error can be avoided with the AddOrReplaceReadGroups which we were already calling but not soon enough. The order is now hanged to avoid these issues.

Release v1.7.0

Non functional changes

• Migrate workflow to DSL 2
• Automated tests on GitHub
• Make conda dependencies at the module level

Functional changes

• Add coverage analysis step based on samtools coverage and samtools depth
• Add step to transform BED file into intervals file

Tronflow BAM preprocessing v1.6.0

Minor changes:

• The output of HsMetrics was missing some fundamental fields, this is corrected now

Tronflow BAM preprocessing v1.5.0

Changes:

• add support for a single input BAM file
• fix realignment step when no known indels are provided

v1.4.0

Changes:

• Improve mark duplicates step performance by ensuring the BAM is query-sorted
• Optionally, remove duplicate reads from output BAMs instead of marking them to reduce the size of output BAMs

v1.3.1

Changes:

• Parametrise computational resources for metrics calculation

v1.3.0

Changes:

• Ensure that metrics are computed on the deduplicated BAM

v1.2.1

Changes:

• Fixes an issue with bad exit code

v1.2.0

• Forces the Java version in the conda environment to openJDK 8
• Fixes an issue with the collection of duplication metrics
• Add parameters for minimum base and mapping quality in the CollectHsMetrics step
• Realignment around indels does not require now the indel resources
• References are not set by default to hg19 now