diff --git a/CHANGELOG.md b/CHANGELOG.md index bde807719..a40e08f50 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/03-amrfinderplus/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/03-amrfinderplus/lablog index 2f002ce77..e12e60c48 100644 --- a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/03-amrfinderplus/lablog +++ b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/03-amrfinderplus/lablog @@ -23,3 +23,14 @@ select bacteria in "${possible_organisms[@]}"; do echo -e "\n\033[0;31mInvalid input.\033[0m" fi done + +cat << "EOF" > _02_amrfinder_summary.sh +#!/bin/bash +output_file="amrfinder_summary.tsv" +{ + for file in *_out.tsv; do + [ "$header_added" ] || { head -n 1 "$file"; header_added=true; } + tail -n +2 "$file" + done +} > "$output_file" +EOF \ No newline at end of file