Update module structure to nf-core

luisas · luisas · commit 4147a2f4790a · 2025-03-18T16:44:20.000+01:00
diff --git a/assets/schema_preprocessing.json b/assets/schema_preprocessing.json
@@ -40,33 +40,30 @@
                 "default": ""
             }
         },
-        "required": [
-            "id",
-            "protocol"
-        ],
+        "required": ["id", "protocol"],
         "allOf": [
             {
                 "if": {
-                "properties": { "protocol": { "const": "ibis" } }
+                    "properties": { "protocol": { "const": "ibis" } }
                 },
                 "then": {
-                "required": ["background_type", "variable", "target"]
+                    "required": ["background_type", "variable", "target"]
                 }
             },
             {
                 "if": {
-                "properties": { "background_type": { "const": "aliens" } }
+                    "properties": { "background_type": { "const": "aliens" } }
                 },
                 "then": {
-                "required": ["background"]
+                    "required": ["background"]
                 }
             },
             {
                 "if": {
-                "properties": { "background_type": { "const": "shade" } }
+                    "properties": { "background_type": { "const": "shade" } }
                 },
                 "then": {
-                "required": ["shade_args"]
+                    "required": ["shade_args"]
                 }
             }
         ],
diff --git a/modules.json b/modules.json
@@ -8,44 +8,32 @@
                     "bedtools/getfasta": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bedtools/shift": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bedtools/slop": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bedtools/subtract": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -54,26 +42,20 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/local/bedtools/random/meta.yml b/modules/local/bedtools/random/meta.yml
@@ -15,42 +15,41 @@ tools:
       documentation: "None"
       tool_dev_url: "None"
       doi: ""
-      licence: ['MIT']
+      licence: ["MIT"]
       identifier: biotools:bedtools
 
 ## TODO nf-core: Add a description of all of the variables used as input
 input:
   #
   ## TODO nf-core: Delete / customise this example input
-    - bam:
-        type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-        ontologies:
-          - edam: "http://edamontology.org/format_25722"
-          - edam: "http://edamontology.org/format_2573"
-          - edam: "http://edamontology.org/format_3462"
-          
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+      ontologies:
+        - edam: "http://edamontology.org/format_25722"
+        - edam: "http://edamontology.org/format_2573"
+        - edam: "http://edamontology.org/format_3462"
 
 ## TODO nf-core: Add a description of all of the variables used as output
 output:
   - bam:
-  #
-  ## TODO nf-core: Delete / customise this example output
-    - "*.bam":
-        type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-        ontologies:
-          - edam: "http://edamontology.org/format_25722"
-          - edam: "http://edamontology.org/format_2573"
-          - edam: "http://edamontology.org/format_3462"
-          
+      #
+      ## TODO nf-core: Delete / customise this example output
+      - "*.bam":
+          type: file
+          description: Sorted BAM/CRAM/SAM file
+          pattern: "*.{bam,cram,sam}"
+          ontologies:
+            - edam: "http://edamontology.org/format_25722"
+            - edam: "http://edamontology.org/format_2573"
+            - edam: "http://edamontology.org/format_3462"
+
   - versions:
-    - "versions.yml":
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 
 authors:
   - "@mathysgrapotte"
diff --git a/modules/local/stimulus/check_model/main.nf b/modules/local/stimulus/check_model/main.nf
@@ -1,4 +1,3 @@
-
 process CHECK_MODEL {
 
     tag "check model"
diff --git a/modules/local/stimulus/split_csv/main.nf b/modules/local/stimulus/split_csv/main.nf
@@ -1,4 +1,3 @@
-
 process STIMULUS_SPLIT_DATA {
 
     tag "${meta.id}-${meta2.id}"
diff --git a/modules/local/stimulus/split_split/main.nf b/modules/local/stimulus/split_split/main.nf
diff --git a/modules/local/stimulus/split_transform/main.nf b/modules/local/stimulus/split_transform/main.nf
diff --git a/modules/local/stimulus/transform_csv/main.nf b/modules/local/stimulus/transform_csv/main.nf
diff --git a/modules/local/stimulus/tune/main.nf b/modules/local/stimulus/tune/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -196,7 +196,6 @@ if (params.genome == null) {
 }
 
 // Load nf-core/deepmodeloptim custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
 // TODO This line can be uncommented once you move the pipeline to nf-core. A file deepmodeloptim.config will be automatically created at the nf-core/configs repo. This is to allow having a pipeline specific config.
 // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/deepmodeloptim.config" : "/dev/null"
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -3,13 +3,7 @@
     "$id": "https://raw.githubusercontent.com/nf-core/deepmodeloptim/master/nextflow_schema.json",
     "title": "nf-core/deepmodeloptim pipeline parameters",
     "description": "nf-core/deepmodeloptim is an end-to-end nextflow based pipeline for statistically testing training procedures of machine learning models",
-    "required": [
-        "data",
-        "data_config",
-        "model",
-        "model_config",
-        "outdir"
-    ],
+    "required": ["data", "data_config", "model", "model_config", "outdir"],
     "type": "object",
     "$defs": {
         "input_output_options": {
@@ -219,14 +213,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -312,4 +299,4 @@
             "default": 300
         }
     }
-}
+}
diff --git a/subworkflows/local/check_model/main.nf b/subworkflows/local/check_model/main.nf
@@ -5,7 +5,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { CHECK_MODEL } from '../../../modules/local/check_model.nf'
+include { CHECK_MODEL } from '../../../modules/local/stimulus/check_model'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/subworkflows/local/shuffle_csv/main.nf b/subworkflows/local/shuffle_csv/main.nf
diff --git a/subworkflows/local/split_csv/main.nf b/subworkflows/local/split_csv/main.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { STIMULUS_SPLIT_DATA } from '../../../modules/local/stimulus_split_csv.nf'
+include { STIMULUS_SPLIT_DATA } from '../../../modules/local/stimulus/split_csv'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/subworkflows/local/split_data_config_split/main.nf b/subworkflows/local/split_data_config_split/main.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { STIMULUS_SPLIT_SPLIT } from '../../../modules/local/stimulus_split_split.nf'
+include { STIMULUS_SPLIT_SPLIT } from '../../../modules/local/stimulus/split_split'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/subworkflows/local/split_data_config_transform/main.nf b/subworkflows/local/split_data_config_transform/main.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { STIMULUS_SPLIT_TRANSFORM } from '../../../modules/local/stimulus_split_transform.nf'
+include { STIMULUS_SPLIT_TRANSFORM } from '../../../modules/local/stimulus/split_transform'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/subworkflows/local/transform_csv/main.nf b/subworkflows/local/transform_csv/main.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { STIMULUS_TRANSFORM_CSV } from '../../../modules/local/stimulus_transform_csv.nf'
+include { STIMULUS_TRANSFORM_CSV } from '../../../modules/local/stimulus/transform_csv'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/subworkflows/local/tune/main.nf b/subworkflows/local/tune/main.nf
@@ -4,7 +4,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { STIMULUS_TUNE } from '../../../modules/local/stimulus_tune.nf'
+include { STIMULUS_TUNE } from '../../../modules/local/stimulus/tune'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Original file line number	Diff line number	Diff line change
`@@ -40,33 +40,30 @@`
`40`	`40`	`"default": ""`
`41`	`41`	`}`
`42`	`42`	`},`
`43`		`- "required": [`
`44`		`- "id",`
`45`		`- "protocol"`
`46`		`- ],`
	`43`	`+ "required": ["id", "protocol"],`
`47`	`44`	`"allOf": [`
`48`	`45`	`{`
`49`	`46`	`"if": {`
`50`		`- "properties": { "protocol": { "const": "ibis" } }`
	`47`	`+ "properties": { "protocol": { "const": "ibis" } }`
`51`	`48`	`},`
`52`	`49`	`"then": {`
`53`		`- "required": ["background_type", "variable", "target"]`
	`50`	`+ "required": ["background_type", "variable", "target"]`
`54`	`51`	`}`
`55`	`52`	`},`
`56`	`53`	`{`
`57`	`54`	`"if": {`
`58`		`- "properties": { "background_type": { "const": "aliens" } }`
	`55`	`+ "properties": { "background_type": { "const": "aliens" } }`
`59`	`56`	`},`
`60`	`57`	`"then": {`
`61`		`- "required": ["background"]`
	`58`	`+ "required": ["background"]`
`62`	`59`	`}`
`63`	`60`	`},`
`64`	`61`	`{`
`65`	`62`	`"if": {`
`66`		`- "properties": { "background_type": { "const": "shade" } }`
	`63`	`+ "properties": { "background_type": { "const": "shade" } }`
`67`	`64`	`},`
`68`	`65`	`"then": {`
`69`		`- "required": ["shade_args"]`
	`66`	`+ "required": ["shade_args"]`
`70`	`67`	`}`
`71`	`68`	`}`
`72`	`69`	`],`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`process CHECK_MODEL {`
`3`	`2`
`4`	`3`	`tag "check model"`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,3 @@`
`1`		`-`
`2`	`1`	`process STIMULUS_SPLIT_DATA {`
`3`	`2`
`4`	`3`	`tag "${meta.id}-${meta2.id}"`
Original file line number	Diff line number	Diff line change
`@@ -196,7 +196,6 @@ if (params.genome == null) {`
`196`	`196`	`}`
`197`	`197`
`198`	`198`	`// Load nf-core/deepmodeloptim custom profiles from different institutions.`
`199`		`-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs`
`200`	`199`	`// TODO This line can be uncommented once you move the pipeline to nf-core. A file deepmodeloptim.config will be automatically created at the nf-core/configs repo. This is to allow having a pipeline specific config.`
`201`	`200`	`// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/deepmodeloptim.config" : "/dev/null"`
`202`	`201`