v3.0.1 bactopia/bactopia "That's My Girl" - 2024/03/25
"That's My Girl" is a phrase my youngest says quite often when playing with her friends
Added
- Updated
bactopia-assembler
to include updated Medaka models - profile for
arcc_hawk
- TB Profiler results are now merged with
collate
command - sample name to plasmidfinder results
- support config files from nf-core/configs
- updated AMRFinder+ database for v3.12.8
- bump program versions in modules
abritamr
: 1.0.14 -> 1.0.17bactopia-assembler
: 1.0.3 -> 1.0.4bactopia-teton
: 1.0.1 -> 1.0.2bactopia-variants
: 1.0.1 -> 1.0.2bakta
: 1.8.2 -> 1.9.3blast
: 2.14.1 -> 2.15.0busco
: 5.5.0 -> 5.7.0gubbins
: 3.3.0 -> 3.3.4multiqc
: 1.15 -> 1.21mashtree
: 1.4.5 -> 1.4.6mykrobe
: 0.12.2 -> 0.13.0ncbi-amrfinderplus
: 3.11.18 -> 3.12.8panaroo
: 1.3.3 -> 1.4.2rgi
: 6.0.2 -> 6.0.3sistr
: 1.1.1 -> 1.1.2stecfinder
: 1.1.0 -> 1.1.1tbprofiler
: 5.0.0 -> 6.1.0
Fixed
- variable name in sketcher module
--para-off
not correctly implemented in PIRATE module- extra space in RGI container image name
- sourmash version STDERR not parsed out
- FASTQC writing to /tmp dir on HPC when non-readable
- abricate and ariba not using output subdirectory
- nextflow tower typos @iferres
- phispy not working with Bakta genbank files
- missed check of
--download_bakta
param in main workflow - quast not working when estimated genome size is 0
abricate
now gets database subdirectories
Enhancements to OSS
- fix amrfinderplus pinning in abritamr bioconda/bioconda-recipes#46714
- adjust python pinning in gubbins bioconda/bioconda-recipes#46713
- fix issue with sistr container bioconda/bioconda-recipes#46712
- update rgi pinning for pyrodigal bioconda/bioconda-recipes#46669
- pin tabix version in snippy bioconda/bioconda-recipes#46458