V.1.5.0

Updated to be compatible with Terra
Removed rMLST typing task
Kraken standard out and error is written to files.

V.1.4.3

bug fix: version number

Features:

• fastqc:0.11.9_plus
• trimmomatic:0.39
• kraken-bracken:k2.1.2-b2.8
• spades:3.15.5
• mlst:2.23.0-2023-07
• quast:5.0.2
• jq:1.6.2
• emmtypingtool:0.0.1
• emmtyper:0.2.0--py_0
• ncbi-amrfinderplus:3.11.11-2023-04-17.1
• mummer:4.0.0-ANI-gbs2

v.1.4.1

Added ani species output result

Features:

• fastqc:0.11.9_plus
• trimmomatic:0.39
• kraken-bracken:k2.1.2-b2.8
• spades:3.15.5
• mlst:2.23.0-2023-07
• quast:5.0.2
• jq:1.6.2
• emmtypingtool:0.0.1
• emmtyper:0.2.0--py_0
• ncbi-amrfinderplus:3.11.11-2023-04-17.1
• mummer:4.0.0-ANI-gbs2

v.1.4.0

New features:

• trimmomatic stats
• MLST
• amrfinder (takes ani species as input)

Features:

• fastqc:0.11.9_plus
• trimmomatic:0.39
• kraken-bracken:k2.1.2-b2.8
• spades:3.15.5
• mlst:2.23.0-2023-07
• quast:5.0.2
• jq:1.6.2
• emmtypingtool:0.0.1
• emmtyper:0.2.0--py_0
• ncbi-amrfinderplus:3.11.11-2023-04-17.1
• mummer:4.0.0-ANI-gbs2

v.1.3.0

Added kraken database as workflow input value
Added ANI docker with complete strep species

features

• rMLST
• ANI
• quast
• emmtyping tool accepts trimmed reads
• fastqc task with coverage using fastqc-scan
• kraken contamination check

software versions

• fastqc:0.11.9_plus
• trimmomatic:0.39
• kraken-bracken:k2.1.2-b2.8
• emmtypingtool:0.0.1
• spades:3.15.5
• emmtyper:0.2.0--py_0
• mummer:4.0.0-ANI-gbs (new)
• quast:5.0.2

v.1.2.0-beta

features

• rMLST
• ANI
• quast
• emmtyping tool accepts trimmed reads
• fastqc task also checks the coverage using fastqc-scan
• trimomatic used updated values
• Added scaffolds to the output (new)

software versions

• fastqc:0.11.9_plus
• trimmomatic:0.39
• kraken-bracken:k2.1.2-b2.8
• emmtypingtool:0.0.1
• spades:3.15.5
• emmtyper:0.2.0--py_0
• mummer:4.0.0-ANI-gas
• quast:5.0.2

v.1.2.0-alpha

Added new features

• rMLST
• ANI
• kraken and bracken (still checking raw and trimmed reads)
• quast
• emmtyping tool accepts trimmed reads
• screen for estimation of coverage (a test)
• fastqc task also checks the coverage using fastqc-scan
• trimomatic used updated values

software versions

• fastqc:0.11.9_plus
• trimmomatic:0.39
• kraken-bracken:k2.1.2-b2.8
• emmtypingtool:0.0.1
• spades:3.15.5
• emmtyper:0.2.0--py_0
• mummer:4.0.0-ANI-gas
• quast:5.0.2

v1.1

Bug fixers on v1.0
Added trimmed reads as the spades input
Added rMLST to the workflow, which was missing in the previous version

v1.0

alpha release v1.0