diff --git a/db-scripts/compute-rds-thresholds.nf b/db-scripts/compute-rds-thresholds.nf index 1facb53..517303a 100644 --- a/db-scripts/compute-rds-thresholds.nf +++ b/db-scripts/compute-rds-thresholds.nf @@ -6,9 +6,9 @@ import java.nio.file.* // Parameters -mpsPath = Paths.get( params.mps ).toRealPath() -contigsPath = Paths.get( params.contigs ).toRealPath() -pcDb = Paths.get( params.pcDb ).toRealPath() +mpsPath = Paths.get( params.mps ).toRealPath() +contigsPath = Paths.get( params.contigs ).toRealPath() +pcDb = Paths.get( params.pcDb ).toRealPath() // Constants @@ -38,7 +38,7 @@ process searchProts { errorStrategy 'retry' maxRetries 3 cpus 1 - memory '2 GB' + memory '2.5 GB' input: set val(type), val(id), val(subSequence) from chContigs @@ -52,7 +52,7 @@ process searchProts { prodigal -i seq.fna -a cdss.faa -p meta if [ -s cdss.faa ] then - diamond blastp --query cdss.faa --db ${pcDB}/mps.dmnd --threads ${task.cpus} --out output.tsv --max-target-seqs 1 --id 90 --query-cover 80 --subject-cover 80 + diamond blastp --query cdss.faa --db ${pcDb} --threads ${task.cpus} --out output.tsv --max-target-seqs 1 --id 90 --query-cover 80 --subject-cover 80 else touch output.tsv fi