v2.1

Features & Fixes:

• New/updated standalone scripts for non-standard inputs
• Added tsv output for placed markers/sequences
• Reporting minimap2 cs tag in marker placement JSON and tsv outputs
• Markerset-based namespace for features #35
• Add dataset type for placed seqs #30
• Fix tsv/json publishDir config
• Fix gzip process not finished on genome annotation features

Data:

• Added Thinopyrum elongatum (tall ryegrass) to triticeae config
• Added IWGSC RefSeq annotations v1.1 to triticeae config

v2.0

• local/remote input agnostic
• workflow test using small eukaryotic genomes
• CI via GitHub actions
• fully containerised
• leaner containers

Input data for test profile

testdata

travis data download and untar

v1.3

New genome assemblies:

• Triticum turgidum subsp. durum (Svevo)
• Triticum aestivum IWGSC RefSeq v2.0 (Chinese Spring) (no gene annotations)

New versions:

• Brachypodium distachyon v3.0 (Ensembl plants release 43)
• Hordeum vulgare (Morex V2)
• Oryza sativa RGAP 7.0 (MSU) (alternative annotations)
• Triticum dicoccoides (Wild emmer) WEW_v2.0 (annotations transferred from v1)

Marker placement included as path in the pipeline

• 90k markers placed on all included genomes #26

Functional changes and assorted bug fixes

• Blocks, Features (genes, markers) and aliases counts recorded per output JSON and distributed in a handful of flat files in the final archive #23
• Consistent use of range and value fields #15
• Multiple annotations per genome allowed for local files #24

Files:

Use the complete data set or the no_LC subset which excludes the low confidence (LC) gene predictions and associated aliases. Refer to doc/upload.md for upload instructions.

v1.1 BUSCO-based pipeline for unannotated genomes

v1.1 BUSCO-based pipeline for un-annotated genomes

Includes JSON files for pretzel, generated from several genome assemblies

To populate your pretzel instance with some pre-computed data, mostly from wheat and related genomes,

1. Download pretzel-genomes-features-aliases-JSON.tar.gz, e.g.

wget https://github.com/plantinformatics/pretzel-input-generator/releases/download/v1.0/pretzel-genomes-features-aliases-JSON.tar.gz

2. Unpack

tar xzvf pretzel-genomes-features-aliases-JSON.tar.gz

3. Follow the upload instructions.