From af4ffc75b0f0995f98304e3e081e3c0b12a81a4c Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Wed, 6 Nov 2024 12:03:40 +0000 Subject: [PATCH] typo in final publish --- modules/vcfpredictModules.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/vcfpredictModules.nf b/modules/vcfpredictModules.nf index 63af962..32d22b9 100644 --- a/modules/vcfpredictModules.nf +++ b/modules/vcfpredictModules.nf @@ -72,7 +72,7 @@ process tbprofiler { label 'new_tmp' publishDir "${params.output_dir}/${sample_name}/antibiogram", mode: 'copy', pattern: '*.tbprofiler-out.json', overwrite: 'true' - publishDir "${params.output_dir}${sample_name}", mode: 'copy', overwrite: 'true', pattern: '*{_err.json,_report.json}' + publishDir "${params.output_dir}/${sample_name}", mode: 'copy', overwrite: 'true', pattern: '*{_err.json,_report.json}' input: tuple val(sample_name), path(minos_vcf), path(report_json), val(isSampleTB) @@ -309,8 +309,8 @@ process finalJson { label 'low_cpu' errorStrategy 'ignore' - - publishDir "${params.output_dir}${sample_name}", mode: 'copy', overwrite: 'true', pattern: '*_report.json' + + publishDir "${params.output_dir}/${sample_name}", mode: 'copy', overwrite: 'true', pattern: '*_report.json' input: tuple val(sample_name), path(vcfmix_json), path(gnomon_json), path(report_json)