3.6.20231219

Minor release:

• updated HeatCluster to 1.0.2
• updated datasets to 15.34.0
• updated blast to 2.15.0
• harmonized pandas containers

3.6.20231205

Minor release:

• updated datasets to 15.31
• updated heatcluster to 0.4.13
• changed phytreeviz and panaroo to staphb's image

3.6.20231121

Changes:

• updated amrfinder to 3.11.26-2023-11-15.1
• updated datasets to 15.29.0-2023-11-21
• added mykrobe
• added drprg
• added mashtree

mykrobe and drprg drug predictions are still in json form in their corresponding directories and are not in the summary file.

3.6.20231115

Notable changes:

• updated blast to 2.14.1
• updated quast to 5.2.0
• added a heatcluster process that takes the SNP matrix from SNP dists and visualizes it

• added a phytreeviz process that takes the newick file from iqtree2 and visualizes it

• added a process to better evaluate the core genome

An example file:

sample,total,core,soft,shell,cloud,per_core,per_soft,per_shell,per_clouc,length,num_ambiguous,per_ambiguous
GCF_000834105.1_ASM83410v1_genomic,776.0,284.0,0.0,309.0,183.0,0.36597938144329895,0.0,0.39819587628865977,0.23582474226804123,275096.0,2750.0,0.00999651030912845
GCF_000972335.1_ASM97233v1_genomic,892.0,284.0,0.0,350.0,258.0,0.3183856502242152,0.0,0.3923766816143498,0.289237668161435,275096.0,6260.0,0.022755692558234217
GCF_000788095.1_ASM78809v1_genomic,3892.0,284.0,0.0,3431.0,177.0,0.07297019527235354,0.0,0.881551901336074,0.045477903391572455,275096.0,4121.0,0.014980225085061215
SRR14436834,3965.0,284.0,0.0,3512.0,169.0,0.07162673392181589,0.0,0.885750315258512,0.04262295081967213,275096.0,5720.0,0.020792741442987175
GCF_900475405.1_44087_C01_genomic,3987.0,284.0,0.0,3567.0,136.0,0.07123150238274392,0.0,0.8946576373212942,0.03411086029596187,275096.0,3272.0,0.011894029720533923
GCF_000758465.1_ASM75846v1_genomic,4017.0,284.0,0.0,3368.0,365.0,0.07069952701020663,0.0,0.838436644261887,0.0908638287279064,275096.0,3497.0,0.012711926018553523
GCF_000978875.1_ASM97887v1_genomic,4189.0,284.0,0.0,3620.0,285.0,0.06779661016949153,0.0,0.8641680592026737,0.0680353306278348,275096.0,5192.0,0.018873411463634512
GCF_000742995.1_ASM74299v1_genomic,4551.0,284.0,0.0,3722.0,545.0,0.06240386728191606,0.0,0.8178422324763788,0.11975390024170512,275096.0,3023.0,0.010988891150725565

• removed the heatcluster python script since heatcluster has a standalone github repo
• !!! CHANGED THE NAME OF A PARAMETER : params.roary_min_genes is now params.min_core_genes !!!
  • this suggests that there will be changes coming to the phylogenetic analysis subworkflow

Non-notable changes:

• add myco_flag for Mycobacterium (am still in the processing of testing modules)
• added drprg, mykrobe, and mashtree processes that aren't connected to anything

3.5.20231024

Minor release:
Updates amrfinder to 3.11.20-2023-09-26.1

3.5.20231017

Minor Update:

• Updated datasets to 15.24.0
• Added some Hafnia and Mycobacterium references for fastani
• Fixed bug #130 when params.msa = true, but no fastani hits were identified

3.5.20231010

Moderate release:

• allows input fasta files via sample sheet (req for cloud)
  • to use set params.fasta_list to the path of a simple text file with one fasta per line
  • more information can be found in the wiki at https://github.com/UPHL-BioNGS/Grandeur/wiki/USAGE
• updated datasets to 15.23.0
• changed how files are decompressed in fastani and named with prokka for msa

WARNING : There is a known bug for those who use Grandeur for when params.msa = true for phylogenetic analysis and there are no fastani hits. Please read #130 for further information and to keep updated.

3.4.20230926

Minor release:

• fixes typo in summary_file.py causing delimiter issues
• updated ncbi-datasets to version 15.20.2
• updated nextflow_schema.json and config template file to harmonize defaults

3.4.20230919

Moderate update - but may come as a great relief to some:

• current-datasets is now set to false by default - this should resolve a lot of issues with connectivity
• changed datasets download to only download new genomes (does not download genomes from list)
  • This retires params.genome_references
• updated fastani to 1.34
• since fastani now allows *.gz as input, the included genomes are now separate compressed files
  • the 'decompression' process was removed
• changed params.fastani_ref to accept a comma-delimited list of fasta files (or fasta.gz files) to be added to the fastani references
• added params.fastani_ref_list to accept a file with a on each line for fasta files (or fasta.gz files) to be added to the fastani references

3.3.20230815

Minor release:

• updated amrfinderplus to 3.11.18-2023-08-08.2