Merge branch 'refactor' into use-nfcore-pipeline-utils-subworkflow

nf-core · Oct 16, 2023 · ce2237e · ce2237e
2 parents 52c4100 + bbc23f0
commit ce2237e
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Showing 12 changed files with 445 additions and 60 deletions.
diff --git a/modules.json b/modules.json
@@ -36,7 +36,12 @@
                     },
                     "nextflowpipelineutils": {
                         "branch": "master",
-                        "git_sha": "76cbb00305f6b045c15c1e202a5bdd516d6f64a3",
+                        "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "nfvalidation_plugin_utils": {
+                        "branch": "master",
+                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
                         "installed_by": ["subworkflows"]
                     },
                     "nfcore_pipeline_utils": {

diff --git a/subworkflows/local/nf_core_fetchngs_utils/main.nf b/subworkflows/local/nf_core_fetchngs_utils/main.nf
@@ -10,7 +10,7 @@
 
 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 { NF_VALIDATION_PLUGIN_UTILS                  } from '../../nf-core/nfvalidation_plugin_utils/main.nf'
 include { 
     NFCORE_PIPELINE_UTILS; 
     workflowCitation; 
@@ -52,7 +52,8 @@ 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/nextflowpipelineutils/tests/main.functions.nf.test b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap b/subworkflows/nf-core/nextflowpipelineutils/tests/main.functions.nf.test.snap
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config b/subworkflows/nf-core/nextflowpipelineutils/tests/nextflow.config
diff --git a/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml b/subworkflows/nf-core/nextflowpipelineutils/tests/tags.yml
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