Checkm2 #95
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Checkm2 #95
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This has to be tested.
mberacochea
approved these changes
May 8, 2024
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Excellent, thanks @tgurbich. The only bit I would correct is the internal db path we have for the checkm2 DB
config/codon_dbs.config
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| @@ -14,4 +14,6 @@ params { | |||
| kegg_classes = "/hps/nobackup/rdf/metagenomics/service-team/production/ref-dbs/genomes-pipeline/kegg_classes.tsv" | |||
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| amrfinder_plus_db = "/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/amrfinderplus/3.11/2023-02-23.1" | |||
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| checkm2_db = "/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/checkm2/CheckM2_database/CheckM2_database/uniref100.KO.1.dmnd" | |||
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We need to normalize that path, it should be
/hps/nobackup/rdf/metagenomics/service-team/ref-dbs/checkm2/<version>/uniref100.KO.1.dmnd
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Good catch, I updated the path.
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Changed the QC tool from CheckM to CheckM2. Enabled NCBI genomes to be processed - NCBI genomes are taken through CheckM2, ENA genomes are expected to have completeness and contamination data provided.