add flag into module processes

Pathogen-Genomics-Cymru · Aug 22, 2024 · 2e0a491 · 2e0a491
1 parent 1795987
commit 2e0a491
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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}