From 14a95f0b9dc16433ceaa7b8b48875ca744b82b36 Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Thu, 5 Dec 2024 13:34:36 +0000 Subject: [PATCH] typo in reafanc --- modules/decontaminationModules.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/decontaminationModules.nf b/modules/decontaminationModules.nf index 3d29f65..0fe0041 100644 --- a/modules/decontaminationModules.nf +++ b/modules/decontaminationModules.nf @@ -262,7 +262,7 @@ process reAfanc { afanc_report = "${sample_name}_afanc_report.json" """ - afanc screen ${afanc_myco_db} ${fq1} ${fq2}-p ${params.afanc.afanc_percent_threshold} \ + afanc screen ${afanc_myco_db} ${fq1} ${fq2} -p ${params.afanc.afanc_percent_threshold} \ -n ${params.afanc.afanc_n_reads_threshold} -o ${sample_name} -t ${task.cpus} -v ${afanc_myco_db}/lineage_profiles/TB_variants.tsv cp ${sample_name}/${sample_name}.json ${sample_name}_afanc_original.json