added python3 containers

phac-nml · Oct 19, 2023 · 37b2f00 · 37b2f00
1 parent f71ec3d
commit 37b2f00
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/nextflow.config b/nextflow.config
@@ -99,7 +99,7 @@ params {
 
 
     // If a param in camel case is present nextflow automatically creates a kebab case parameter as well
-    schema_ignore_params       = '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'
+    schema_ignore_params       = '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'
 
     stage_in_mode = 'symlink'
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -2587,6 +2587,16 @@
             "type": "string",
             "default": "PointfinderDB",
             "hidden": true
+        },
+        "python3.singularity": {
+            "type": "string",
+            "default": "https://depot.galaxyproject.org/singularity/python%3A3.10.4",
+            "hidden": true
+        },
+        "python3.docker": {
+            "type": "string",
+            "default": "docker://python/python:3.10.4-alpine3.16",
+            "hidden": true
         }
     }
 }