CI
23bf721768
Build pipeline: viash-hub.demultiplex.add-transfer-completed-file-pwqjk
Source commit: e7ed491011
Source message: Update CHANGELOG
34 lines
1.3 KiB
Bash
Executable File
34 lines
1.3 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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declare -A input_output_mapping=(["par_input"]="par_output"
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["par_input_multiqc"]="par_output_multiqc"
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["par_input_run_information"]="par_output_run_information"
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["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs"
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)
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for input_argument_name in "${!input_output_mapping[@]}"
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do
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input_location="${!input_argument_name}"
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output_argument_name="${input_output_mapping[$input_argument_name]}"
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output_location="${!output_argument_name}"
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echo "Publishing $input_location -> $output_location"
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echo "Creating directory if it does not exist."
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mkdir -p $(dirname "$output_location") && echo "Containing directory $output_location created"
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echo "Copying files..."
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cp -rL "$input_location" "$output_location"
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echo "Output files for $output_location:"
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ls "$output_location"
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done
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echo "Grouping output from $par_input_sample_qc into $par_output_sample_qc"
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mkdir -p "$par_output_sample_qc"
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IFS=";" read -ra sample_qc_inputs <<< $par_input_sample_qc
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for qc_dir in "${sample_qc_inputs[@]}"; do
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echo "Copying contents of $qc_dir"
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find -H -D exec "$qc_dir" -type f -maxdepth 1 -exec cp -t "$par_output_sample_qc" {} +
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done |