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Emmtyper characterization template - Fixed path to blast database and update params #339

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Sep 12, 2024
Merged

Emmtyper characterization template - Fixed path to blast database and update params #339

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07a3eb1
fixed path database and update emmtyper params
Daniel-VM Sep 12, 2024
62d9aaf
update changelog #339
Daniel-VM Sep 12, 2024
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,8 +9,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
### Credits

Code contributions to the new version:
- [Daniel Valle](https://github.com/Daniel-VM)


### Template fixes and updates
- Fixed path to blast database and update Emmtyper params [#339](https://github.com/BU-ISCIII/buisciii-tools/pull/339)

### Modules

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8 changes: 4 additions & 4 deletions bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog
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Expand Up @@ -53,7 +53,7 @@ cat <<EOF > _01_emmtyper.sbatch
# create results folder
mkdir -p 01-typing
mkdir -p 01-typing/tmps
blastdb_path=/data/bi/references/cdc_emm_blastdb
blastdb_path=/data/bi/references/cdc_emm_blastdb/20240509

# Run emmtyper
singularity exec \\
Expand All @@ -63,9 +63,9 @@ singularity exec \\
/data/bi/pipelines/singularity-images/singularity-emmtyper.0.2.0--py_0 emmtyper \\
-w blast \\
--keep \\
--blast_db "\${blastdb_path}/cdc_emm_database29042024" \\
--percent-identity 95 \\
--culling-limit 5 \\
--blast_db "\${blastdb_path}/cdc_emm_database" \\
--percent-identity 100 \\
--culling-limit 5 \
--output 01-typing/results_emmtyper.out \\
--output-format verbose \\
./fasta_inputs/*.fasta
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