3.3.0 - bwakit post-processing

Update PCAP-core to 5.7.0, which includes bwakit post-processing.

3.2.0 - features and maint

See PCAP-core CHANGES between 4.4.0-5.4.0 - note that bwa-mem2 is only applied on request and is NOT considered ready for production at this time.

New options have been exposed to the CWL mappings.

3.1.4 - Speed and security

• Update to build process to ensure security patches are added on each new release.
• Core threaded routine modified to speedup resumption of jobs (PCAP-code).
• Speedup of bamsort by adding helper threads (PCAP-code).

3.1.0 - undergoing final verification

Please do not use until we remove the pre-release tag.

3.0.1 - add csi index input support

• Change to forked Bio::DB::HTS so csi indexed of BAM files can be used in downstream images.

3.0.0

• Drop pre/post exec functions in mapping.sh
• Add ability to pair a groups file with fastq inputs to add info to readgroups
  in final BAM/CRAM files (PCAP-core).
• BWA 0.7.17 - bug fixes for future alpine building.
• Biobambam2 2.0.84 - via pre-compiled versions
• HTSlib + Samtools 1.7
• PCAP-core 4.1.1
  • mismatchQc options added
• cgpBigWig 1.0.0 (via dockstore-cgpbigwig 2.0.0)
• Examples moved to more useful naming, now have:
  • examples/bamOutput and examples/cramOutput each containing:
    • bam_input.json
    • fastq_gz_input.json - with yaml groupinfo file example.
• Multiple CWL descriptors one for BAM output, another for CRAM, legacy version retained.
  • Ensure you use the correct json examples.
• Now using secondaryFiles for outputs to reduce repetitive entries in cwl and json.
  • Bugfix to dockstore tool needed for output provisioning, 1.3.6+

HotFix - moves test data to a permanent home

Old ftp location for bam/cram would expire data after 3 months.

Shrink docker images

• PCAP-core forked to cancerit and all legacy PCAWG code removed.
• Update to cgpBigWig/libBigWig to handle bug detected in ASCAT.
• First layer of streamlined install process to reduce build time of dependant images.
• Biobambam2 now building from source (previously picked up precompiled 'etch').

1.0.8

bwa_mem.pl

Fixes bug resulting in sample name not being assigned to mapped BAM header when input BAM has no SM tag in the readgroup header.

1.0.0 - initial release

Initial release of mapping workflow for use in PanProstate project (plus a base for other Sanger anaysis)