updated schema

phac-nml · Dec 8, 2023 · df5ec33 · df5ec33
1 parent 5aa2cd3
commit df5ec33
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -58,7 +58,7 @@ params {
 
     validationS3PathCheck = true
     // Can probably remove with other nf-core stuff
-    validationSchemaIgnoreParams = 'coverage_calc_fields.fixed_cov,coverage_calc_fields.auto_cov,assembly_status.report_tag,medaka.model,medaka,validation-S3Path-check,validationS3PathCheck,abricate,python3,pointfinder_db_tag,staramr,mobsuite_recon,skip_staramr,genomes,flye_read_type,shigeifinder,lissero,sistr,ectyper,bandage,bakta,unicycler,medaka,pilon_iterative,pilon,racon,samtools,minimap2,r_contaminants,mash,kraken,checkm,quast_filter,quast,fastqc,spades,flye,chopper,fastp,seqtk,seqtk_size,kat,coreutils,opt_platforms,QCReportFields,QCReport-fields,QCReport,kraken_bin,shigatyper,spatyper,kleborate,subtyping_report,kraken_species,top_hit_species,mash_meta,mlst,raw_reads,abricate_params,target_depth'
+    validationSchemaIgnoreParams = 'filtered_reads,coverage_calc_fields,assembly_status,coverage_calc_fields.fixed_cov,coverage_calc_fields.auto_cov,assembly_status.report_tag,medaka.model,medaka,validation-S3Path-check,validationS3PathCheck,abricate,python3,pointfinder_db_tag,staramr,mobsuite_recon,skip_staramr,genomes,flye_read_type,shigeifinder,lissero,sistr,ectyper,bandage,bakta,unicycler,medaka,pilon_iterative,pilon,racon,samtools,minimap2,r_contaminants,mash,kraken,checkm,quast_filter,quast,fastqc,spades,flye,chopper,fastp,seqtk,seqtk_size,kat,coreutils,opt_platforms,QCReportFields,QCReport-fields,QCReport,kraken_bin,shigatyper,spatyper,kleborate,subtyping_report,kraken_species,top_hit_species,mash_meta,mlst,raw_reads,abricate_params,target_depth'
     validationFailUnrecognisedParams = false // for the qcreport fields
     //schema_ignore_params = 'validation-S3Path-check,validationS3PathCheck,abricate,python3,pointfinder_db_tag,staramr,mobsuite_recon,skip_staramr,genomes,flye_read_type,shigeifinder,lissero,sistr,ectyper,bandage,bakta,unicycler,medaka,pilon_iterative,pilon,racon,samtools,minimap2,r_contaminants,mash,kraken,checkm,quast_filter,quast,fastqc,spades,flye,chopper,fastp,seqtk,kat,coreutils,opt_platforms,QCReportFields,QCReport-fields,QCReport,kraken_bin,shigatyper,spatyper,kleborate,subtyping_report,kraken_species,top_hit_species,mash_meta,mlst,raw_reads,abricate_params,target_depth'
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -2795,6 +2795,16 @@
             "type": "string",
             "default": "AssemblyCompleted",
             "hidden": true
+        },
+        "filtered_reads.threshold": {
+            "type": "integer",
+            "default": 1000,
+            "hidden": true
+        },
+        "filtered_reads.report_tag": {
+            "type": "string",
+            "default": "MeetsReadThreshold",
+            "hidden": true
         }
     }
 }