v1.0.5

v1.0.5

This release adds workflows for transmission analysis from plate swipe data based on StrainGE.

Changes

• Added three new workflows: GEMSTONE_StrainGR, StrainGR_prepare, and StrainGR_compare. GEMSTONE_StrainGR does pairwise comparison of genetic distances between strains in a set of plate swipes with StrainGR. StrainGR_prepare, and StrainGR_compare and two modules of GEMSTONE_StrainGR which do variant calling per sample and pairwise comparisons, respectively.

v1.0.4

v1.0.4

v1.0.3

This release implements minor changes to the GEMSTONE_Plate_Swipes_Illumina_PE workflow relative to v1.0.3. These changes are aimed at increasing the requested memory for some QC tasks, as well as dynamically determining the amount of memory to request.

Changes

• Increase the mem in the BBDuk task in the read_QC_trim workflow.

• Make the requested mem for trimmomatic and ncbi_scrub in the read_QC_trim workflow dependent on the input file sizes.

• Updated the documentation.

v1.0.2

v1.0.2

This release implements minor changes to v1.0.1. These changes are aimed at reducing storage and computation costs.

Changes

• Added qc_only flag to GEMSTONE_Plate_Swipes_Illumina_PE (set to true by default). If this option is set to true, the workflow does not assemble genomes, only doing QC and taxon estimation with Kraken2/Braken.
• Fixed #3 by changing the type of the selected StrainGST database outputs from Array[File] and File to Array[String] and String.
• Updated the documentation.

Full Changelog: v1.0.1...v1.0.2

v1.0.1

Changelog

Major changes affect the StrainGE tasks and workflow:

1. The StrainGE task now accepts zstandard-compressed tar archived databases instead of tar archives compressed with gzip.
2. StrainGR steps in the StrainGE task are now optional. If strainge_prepare_straingr is set to false, decreases computation time to about 1/10 when compared to when strainge_prepare_straingr is true.

v1.0.0

GEMSTONE workflows v1.0.0

First release of WDL workflows for the GEMSTONE project. Includes workflows to process Illumina paired-end reads from isolates and plate swipes. These workflows are based on the PHB workflows by Theiagen. Workflows for useful standalone tools are also provided, namely StrainGE for strain level detection, Kraken/Bracken2 for abundance estimation, and metaWRAP for MAG binning and refinement.

Changes

None

v0.0.2

Update .dockstore.yml

v0.0.1beta

Update .dockstore.yml