Added shared conda env location

WEHIGenomicsRnD · Feb 26, 2024 · 153df48 · 153df48
1 parent dbadb08
commit 153df48
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Showing 3 changed files with 28 additions and 9 deletions.
diff --git a/modules/trim.nf b/modules/trim.nf
@@ -3,7 +3,9 @@ process trim_primer {
 
     publishDir params.outdir, mode: 'copy'
 
-    conda "${projectDir}/envs/biopython.yaml"
+    conda "${ params.conda_env_location != null && params.conda_env_location != '' ?
+              params.conda_env_location + '/biopython' :
+              projectDir + '/envs/biopython.yaml' }"
 
     input:
     path fastq

diff --git a/nextflow.config b/nextflow.config
@@ -15,7 +15,7 @@ params {
 
     index_template_file     = "$projectDir/.test/data/indexes.txt"
 
-    demultiplex             = true
+    demultiplex             = false
 
     //number of bases to search for index 1 at start of read
     bases_num_r1            = 12
@@ -30,6 +30,9 @@ params {
     //if false, the database is queried to create one
     //if true, config.txt should be in the input directory
     is_config_file_provided = true
+
+    // if specified, use this location to load prebuilt conda environments
+    conda_env_location      = ""
 }
 
 //SQL DB Plugin

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -110,13 +110,24 @@
                     "default": false,
                     "description": "Optional ready-made config file for splitcode. Use this to skip the databse index lookup. Must be called config.txt and put in input directory."
                 }
-            },
-            "required": [
-                "fwd_primer",
-                "rev_primer",
-                "primer_mismatches",
-                "barcode_length"
-            ]
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "conda_env_location": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "Use this location for pre-build conda environments (if blank, new conda environments will be created).",
+                    "fa_icon": "fas fa-cog",
+                    "default": "",
+                    "hidden": true
+                }
+            }
         }
     },
     "allOf": [
@@ -128,6 +139,9 @@
         },
         {
             "$ref": "#/definitions/demultiplex_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
         }
     ]
 }