metaBIOMX 1.0.0

v1.0.0 - [2025-07-07]

Added

• docker and singularity support
• Custom docker scripts can be found in path /containers/docker
• Overview of process and additional container & argument specification in /conf/containers.config
• NF-core modules and local modules
• CHECK_INPUT subworkflow for params validation
• subworkflows for decontamination and read_annotation
• main.nf that calls the workflow/metapipe.nf
• Contig annotation subworkflow.
• combine trim & decon reads into an overview
• NF-core compatible pipeline initialisation & validation
• simple unit-testing for each subworkflow
• BIOM OUTPUT in read_annotation and contig_annotation
• #4 Added default configure of databases

Changed

• Repo structure adapted, and similar to nf-core pipelines
• Local modules follow same design as NF-core modules
• updated Humann2 to Humann3
• updated chocophlan, uniref90 and utility_mapping databases
• decontamination from BBDuk to Kneaddata (uses BMtagger and Bowtie2) with new hg38 database.
• Singularity images are not downloaded in a singularity cacheDir to be specified by the user.
• Error handling of configure

Fixed

• #6 duplicate headers from spades