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Updated 03-amrfinderplus lablog (characterization template) #407

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merged 4 commits into from
Jan 17, 2025
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Updated 03-amrfinderplus lablog (characterization template) #407

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599cec1
Updated characterization/03-amrfinderplus lablog
Aberdur Jan 17, 2025
6d8c896
Update CHANGELOG
Aberdur Jan 17, 2025
ed15949
Update CHANGELOG
Aberdur Jan 17, 2025
d4f15c4
Deleted variable not used
Aberdur Jan 17, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

- User added to sftp_user.json [#404] (https://github.com/BU-ISCIII/buisciii-tools/pull/404).
- Fix archived path [#405](https://github.com/BU-ISCIII/buisciii-tools/pull/405)
- Updated characterization/03-amrfinderplus lablog with summary generator [#406](https://github.com/BU-ISCIII/buisciii-tools/pull/406)

### Modules

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12 changes: 12 additions & 0 deletions ...i/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/03-amrfinderplus/lablog
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Expand Up @@ -23,3 +23,15 @@ select bacteria in "${possible_organisms[@]}"; do
echo -e "\n\033[0;31mInvalid input.\033[0m"
fi
done

cat << "EOF" > _02_amrfinder_summary.sh
#!/bin/bash
output_file="amrfinder_summary.tsv"
{
for file in *_out.tsv; do
sample_name=$(basename "$file" "_out.tsv")
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[ "$header_added" ] || { head -n 1 "$file"; header_added=true; }
tail -n +2 "$file"
done
} > "$output_file"
EOF
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