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3.4.0

  • NOT FULLY TESTED
  • Change base image for Dockerfile to PCAP-core 5.8.1 (htslib update - 1.20)

3.3.0

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

3.2.0

  • Update PCAP-core to 5.4.0, new ubuntu htslib/samtools 1.11.
  • -scramble deprecated, see seqslice
  • New options to control duplicate marking

3.1.4

  • Update PCAP-core to 4.3.5
    • Speedup bamsort by adding sort helpers

3.1.3

  • Update PCAP-core to 4.3.4
    • More stability work on Threaded for singularity/docker

3.1.2

  • Update PCAP-core to 4.3.3
  • Update base image to 2.1.1 (dockstore-cgpbigwig)
  • Add security updates to docker build process

3.1.1

  • Update PCAP-core to 4.3.2
    • Much faster to resume a partial job
    • Fixes for CRAM handling in mismatchQc/mmFlagModifier

3.1.0

  • Update to dockstore-cgpbigwig:2.1.0 for base image
  • Update dependencies:
    • gt1/biobambam2 - 2.0.87
    • HTSLib - 1.9
    • Samtools -1.9
    • Bio::DB::HTS - 2.10
    • PCAP-core - 4.3.1
  • Drop expected tree, will be revising how verification of container is achieved.

3.0.4

  • Update to dockstore-cgpbigwig:2.0.1 for base image

3.0.3

  • Switch back to Ensembl Bio::DB::HTS now merged

3.0.2

  • v4.2.0 of PCAP-core to allow use of threads for bam_stats

3.0.1

  • 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+

2.0.1

  • Test data in examples/sample_configs.local.json moved to a non-expiring location.

2.0.0

  • 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

Fix in PCAP-core to handle passing of sample name when input BAM has no SM tag in header.

1.0.7

HTSlib upgades in toolset for consistency.

1.0.6

Bump PCAP-core version to fix fastq input handling

1.0.5

Adds travis-ci

1.0.4

Bad versions in 1.0.3

1.0.3

Base PCAP-core upgraded to improve mapping through-put and CPU use.

1.0.2

Added build badges

1.0.1

Fix CWL to get description to display on Dockstore.org

1.0.0

Initial release. Fully functional.