Jetstream Resources v1.2.2

Notable changes:

• Many shell scripts have permission updates to 755 for consistency with other scripts in the repository
• Capture kit definition updates for coyote, phoenix, and tempe
• SigProfiler script updates to only run mutational matrix generation and extraction (useful for genomes that are not supported in cosmic)
• Resource usage reporting scripts are now more dynamic and a bit smarter
  • Automatically grouping tasks based on task tags
  • Launcher script checks to make sure that the python version used has jetstream installed
• Tempe has updated bwa index generation scripts to make sure that the generated index is alt-aware
  • Tempe script usage order in README has been updated to reflect path changes

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Expected to support the following pipelines (likely supports lower versions as well):

• Tempe >=v1.2.0
• Phoenix v1.2.0
• Suncity v1.2.1
• Coyote v1.2.1
• Private repositories ^{until extensively tested in a production capacity}
  • Sonoran v1.2.1
  • Bastien v1.2.2
  • Monte v1.2.2

Jetstream Resources v1.2.1

This release expands support for newly created pipelines and adds some more generics.

Notably this adds supporting scripts for Tempe, Sonoran, Bastien, and Monte as well as a handful of capture kit definition updates.

In total this supports:

• Tempe v1.0.1-v1.1.2
• Phoenix v1.2.0
• Suncity v1.2.1
• Coyote v1.2.1
• Private repositories ^{until extensively tested in a production capacity}
  • Sonoran v1.2.1
  • Bastien v1.2.2
  • Monte v1.2.2

Jetstream Resources v1.2.0

This release supports workflows used in the v1.2.x Jetstream workflows (Phoenix, Suncity, Coyote).

Issues resolved in this release:

• CDS PADDED FILES FOR TMB #50
• Update Salmon for non-phoenix workflows #33
• Suncity and non-phoenix HARD PATH VARIABLES #19
• gnomad VCF includes all variants #4

JetStream Resources v0.4.0

First formal release, includes all resources used for Phoenix v0.4.3 and earlier.