From 2e0a491738f0633aa58a8eefe35ae751fa25c9a6 Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Thu, 22 Aug 2024 08:22:10 +0000 Subject: [PATCH] add flag into module processes --- modules/decontaminationModules.nf | 4 ++-- modules/preprocessingModules.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/decontaminationModules.nf b/modules/decontaminationModules.nf index 1cbd656..53594a2 100644 --- a/modules/decontaminationModules.nf +++ b/modules/decontaminationModules.nf @@ -34,7 +34,7 @@ process identifyBacterialContaminants { report_json = "${sample_name}_report.json" """ - identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} null + identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} null ${params.permissive} contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${sample_name}_species_in_sample.json) acceptable_species=\$(jq -r '.summary_questions.is_the_top_species_appropriate' ${sample_name}_species_in_sample.json) @@ -348,7 +348,7 @@ process summarise { report_json = "${sample_name}_report.json" """ - identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} ${prev_species_json} + identify_tophit_and_contaminants2.py ${afanc_json} ${kraken_json} ${refseq} ${params.species} ${params.unmix_myco} ${resources} ${prev_species_json} ${params.permissive} contam_to_remove=\$(jq -r '.summary_questions.are_there_contaminants' ${sample_name}_species_in_sample.json) diff --git a/modules/preprocessingModules.nf b/modules/preprocessingModules.nf index 3cf7b6a..504ef8b 100644 --- a/modules/preprocessingModules.nf +++ b/modules/preprocessingModules.nf @@ -374,7 +374,7 @@ process afanc { cp ${sample_name}/${sample_name}.json ${sample_name}_afanc_original.json reformat_afanc_json.py ${sample_name}/${sample_name}.json - identify_tophit_and_contaminants2.py ${afanc_report} ${kraken_json} $refseq_path ${params.species} ${params.unmix_myco} $resource_dir null + identify_tophit_and_contaminants2.py ${afanc_report} ${kraken_json} $refseq_path ${params.species} ${params.unmix_myco} $resource_dir null ${params.permissive} echo '{"error":"Kraken's top family hit either wasn't Mycobacteriaceae, or there were < 100k Mycobacteriaceae reads. Sample will not proceed further than afanc."}' | jq '.' > ${error_log} && printf "no" && jq -s ".[0] * .[1] * .[2]" ${software_json} ${error_log} ${sample_name}_species_in_sample.json > ${report_json}