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Make use of prefix and support gzipped input #5424

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Make use of prefix and support gzipped input #5424

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55dac18
Make use of prefix and support gzipped input
gariem Apr 3, 2024
ca62890
Update format, fix file deletion
gariem Apr 23, 2024
978f616
Remove temporary file. Ignore if doesn't exists
gariem Apr 29, 2024
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31 changes: 21 additions & 10 deletions modules/nf-core/iphop/predict/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@ process IPHOP_PREDICT {
path iphop_db

output:
tuple val(meta), path("Host_prediction_to_genus_m*.csv") , emit: iphop_genus
tuple val(meta), path("Host_prediction_to_genome_m*.csv") , emit: iphop_genome
tuple val(meta), path("Detailed_output_by_tool.csv") , emit: iphop_detailed_output
tuple val(meta), path("*.Host_prediction_to_genus_m*.csv") , emit: iphop_genus
tuple val(meta), path("*.Host_prediction_to_genome_m*.csv") , emit: iphop_genome
tuple val(meta), path("*.Detailed_output_by_tool.csv") , emit: iphop_detailed_output
path "versions.yml" , emit: versions

when:
Expand All @@ -25,17 +25,28 @@ process IPHOP_PREDICT {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
export PERL5LIB=/usr/local/lib/perl5/site_perl/5.22.0

INPUT=$fasta
if [[ $fasta == *.gz ]]
then
gunzip -c $fasta > ${prefix}.fasta
INPUT=${prefix}.fasta
fi

iphop \\
predict \\
--fa_file $fasta \\
--fa_file \$INPUT \\
--out_dir iphop_results \\
--db_dir $iphop_db \\
--num_threads $task.cpus \\
$args

mv iphop_results/Host_prediction_to_genus_m*.csv .
mv iphop_results/Host_prediction_to_genome_m*.csv .
mv iphop_results/Detailed_output_by_tool.csv .
for FILE in iphop_results/Host_prediction_to_*.csv; do
mv \${FILE} ./${prefix}.\${FILE##*/}
done

mv iphop_results/Detailed_output_by_tool.csv ./${prefix}.Detailed_output_by_tool.csv
rm -f ${prefix}.fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -49,9 +60,9 @@ process IPHOP_PREDICT {
def min_score = args.contains('--min_score') ? args.split('--min_score ')[1] : '90'
"""
mkdir -p iphop_results
touch Host_prediction_to_genus_m${min_score}.csv
touch Host_prediction_to_genome_m${min_score}.csv
touch Detailed_output_by_tool.csv
touch ${prefix}.Host_prediction_to_genus_m${min_score}.csv
touch ${prefix}.Host_prediction_to_genome_m${min_score}.csv
touch ${prefix}.Detailed_output_by_tool.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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