Merge pull request #222 from nf-core/use-nfcore-validation-subworkflow

Use nf-core nfvalidation subworkflow
nf-core · Oct 16, 2023 · c6714cd · c6714cd
2 parents 96a6708 + 94d75cb
commit c6714cd
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Showing 8 changed files with 441 additions and 55 deletions.
diff --git a/modules.json b/modules.json
@@ -38,6 +38,11 @@
                         "branch": "master",
                         "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3",
                         "installed_by": ["subworkflows"]
+                    },
+                    "nfvalidation_plugin_utils": {
+                        "branch": "master",
+                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -9,8 +9,8 @@
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS                 } from '../../../modules/nf-core/custom/dumpsoftwareversions'
-include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion } from '../../nf-core/nextflowpipelineutils/main'
-include { NF_VALIDATION_PLUGIN_UTILS                  } from '../nf_validation_plugin_utils'
+include { NEXTFLOW_PIPELINE_UTILS; getWorkflowVersion  } from '../../nf-core/nextflowpipelineutils/main'
+include { NF_VALIDATION_PLUGIN_UTILS                  } from '../../nf-core/nfvalidation_plugin_utils/main.nf'
 include { NF_CORE_PIPELINE_UTILS; workflowCitation; nfCoreLogo; dashedLine; completionEmail; completionSummary; imNotification } from '../nf_core_pipeline_utils'
 
 /*
@@ -44,7 +44,8 @@ workflow PIPELINE_INITIALISATION {
         workflow_command,
         pre_help_text,
         post_help_text,
-        params.validate_params
+        params.validate_params,
+        "nextflow_schema.json"
     )
 
     //

diff --git a/subworkflows/local/nf_validation_plugin_utils/main.nf b/subworkflows/local/nf_validation_plugin_utils/main.nf
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf b/subworkflows/nf-core/nfvalidation_plugin_utils/main.nf
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml b/subworkflows/nf-core/nfvalidation_plugin_utils/meta.yml
diff --git a/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test b/subworkflows/nf-core/nfvalidation_plugin_utils/tests/main.nf.test