From 3e84eb082b5d5cba89fcc644c0f1b91686a0fcd6 Mon Sep 17 00:00:00 2001 From: Sebastian Krautwurst Date: Fri, 22 Apr 2022 10:20:33 +0200 Subject: [PATCH 1/2] add threshold params --- CholerAegon.nf | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/CholerAegon.nf b/CholerAegon.nf index 84ee689..03f893c 100644 --- a/CholerAegon.nf +++ b/CholerAegon.nf @@ -13,6 +13,9 @@ params.shortreads = false params.do_all_assemblies = false +params.min_coverage_percent = 80. +params.min_identity_percent = 80. + // channels @@ -337,7 +340,11 @@ process combine_results { tuple val(name), val(type), path("${name}_${type}_combined_results.csv") script: """ - combine_results.py --rgi_results ${rgi_results} --abricate_results ${abricate_results} --output ${name}_${type}_combined_results + combine_results.py --rgi_results ${rgi_results} \ + --abricate_results ${abricate_results} \ + --output ${name}_${type}_combined_results \ + --coverage_threshold ${params.min_coverage_percent} \ + --identity_threshold ${params.min_identity_percent} """ } From 9bca568c1f3a8a77424d13f094b56271d2697d7c Mon Sep 17 00:00:00 2001 From: Sebastian Krautwurst Date: Fri, 22 Apr 2022 10:25:20 +0200 Subject: [PATCH 2/2] defaults fix --- CholerAegon.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CholerAegon.nf b/CholerAegon.nf index 03f893c..773eee0 100644 --- a/CholerAegon.nf +++ b/CholerAegon.nf @@ -13,8 +13,8 @@ params.shortreads = false params.do_all_assemblies = false -params.min_coverage_percent = 80. -params.min_identity_percent = 80. +params.min_coverage_percent = 80 +params.min_identity_percent = 80 // channels