v1.1.1

This patch release implements several enhancements and improvements to the phylogenetic workflows

For the kSNP3, Mashtree, and Core_Gene_SNP workflows, several changes have been implemented.

A new task was created, reorder_matrix that performs the following:

1. Phylogenetic trees have been midpoint-rooted to improve appearance. Final trees from these workflows are now midpoint-rooted.
2. Previously, SNP matrices were not ordered. Now, they are ordered to match the order of terminal ends in the midpoint-rooted phylogenetic tree.
3. Phandango coloring is automatically applied to all column headers in matrices (:c1); these matrix files are .csv files for easy transfer/upload to Phandango.

A new task was created, summarize_data that performs the following:

1. Digests a comma-separated list of column names
2. Parses through those column contents
3. Outputs a .csv file that indicates presence (TRUE)/absence (empty cell) for each item in those columns.
4. A Boolean option phandango_coloring will color all items from the same column in the same format; rows are ordered according to the terminal ends of the midpoint-rooted tree for easy transfer/uplod to Phandango.

These two tasks have been added to all three phylogenetic workflows in the PHBG repository.

Other modifications

ShigEiFinder

A new optional task was created that allows ShigEiFinder to be run with read files as inputs instead of assemblies. 10 new output columns were created that are identical to the task that uses assemblies as input except they have the _reads suffix to differentiate between them. To use, set the new optional input variable call_shigeifinder_reads_input to true. This task is not run by default.

AMRFinderPlus

A typo has been corrected in the AMRFinderPlus task; the previous "pnemoniae" has now been corrected to "pneumoniae"

New TheiaProk QC

Several new columns are now being outputted that report the following:

• r1, r2, and combined raw mean quality scores and read lengths
• combined clean mean quality scores and read lengths (no individual r1 and r2 to avoid excessive column creep)

Clean mean quality scores and read lengths are now able to be checked in the qc_check task as well.

What's Changed

• Update task_amrfinderplus.wdl by @kevinlibuit in #204
• add optional task for shigeifinder w/ reads as input; update default docker for both shigeifinder & shigatyper by @kapsakcj in #202
• Fja readlength dev by @frankambrosio3 in #201
• reorder snp matrix by @sage-wright in #198

Full Changelog: v1.1.0...v1.1.1

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