phoenix_v0.4.1

CMD Changes - Will cause restarts

• Bug fix within pairoscope for when grep returns 0 results
• Bug fix within samtools stats task from bam_qc_all.jst will now sort the intersection of bedtools merge to ensure correct order

Other Changes

• Optimized gatk metrics cpu and memory usage (8 --> 2 cpus)

phoenix_v0.4.0

New Features

• Implemented pairoscope workflow for myeloma immunoglobulin translocation detection
• We now generate symbolic links to files that would be commonly used

CMD Changes - Will cause restarts

• Updated bcftools to 1.10.1 (fixes 64-bit issue identified in v1.10.0)
• Updated htslib to 1.10.1 (fixes 64-bit issue identified in v1.10.0)
  • added htslib module load were appropriate, as it no longer loads by default with bcftools
• Updated vcfMerger2 to v0.8.7 (fixes edge case in octopus)
• Changed deepvariant module cmd, removed redundant singularity module load
• Changed samtools stats cmd, to support future QC process
• Changed ichor cmd, added .ichor. to output filenames

Other Changes

• Changed bwa_fixmate_sort directive, increased memory request to 50Gb)
• Added support for using bait/probe files in hsMetrics
• Optimized delly cpu usage (8 --> 2 cpu)
• Set delly memory request (16Gb)

phoenix_v0.3.1

Other Changes

• Removed temp file deletion task from post markdup step as it runs in base_recalibration steps, prevents task fail created by redundant tasks.

phoenix_v0.3.0

CMD Changes - Will cause restarts

• Updated samtools to v1.10 (finally a new version after 18 months)

  • Removes need for nightly build used for markdup

• Various edge case bugfixes.

  • Updated VcfMerger2.0 to version8.5 (Significant change, replaces bcftools reserved key "TYPE" to VTYPE to prevent errors with bcftools)

phoenix_v0.2.5

Bug fixes over v0.2.4

• Updated VcfMerger2.0 to version 8.3

phoenix_v0.2.4

Fixed issues within delly's temp_dir structure

phoenix_v0.2.3

Bug fixes for star fusion and delly directory tree.

phoenix_v0.2.2

Updates to improve future maintainability and bugfixes.

phoenix_v0.2.1

This is a pre release intended to start analysis on the MMRF data set.

phoenix_v0.2.0

This is a pre release intended to start analysis on the MMRF data set.