Huge effort to finally update modules done :)

nrhorner · Aug 17, 2023 · 4e1779d · 4e1779d
1 parent 6f3d36b
commit 4e1779d
Show file tree

Hide file tree

Showing 141 changed files with 1,804 additions and 1,825 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1 +1,15 @@
 repository_type: pipeline
+lint:
+  files_exist:
+    - conf/modules.config
+    - conf/test.config
+    - conf/test_full.config
+  files_unchanged:
+    - assets/multiqc_config.yml
+    - assets/nf-core-sarek_logo_light.png
+    - docs/images/nf-core-sarek_logo_dark.png
+    - docs/images/nf-core-sarek_logo_light.png
+    - lib/NfcoreTemplate.groovy
+    - lib/NfcoreSchema.groovy
+  schema_params: False
+  template_strings: False
diff --git a/conf/modules.config → conf/modules/modules.config b/conf/modules.config → conf/modules/modules.config
diff --git a/conf/slurm.config b/conf/slurm.config
diff --git a/conf/tcga.config b/conf/tcga.config
diff --git a/conf/tcga2.config b/conf/tcga2.config
diff --git a/conf/tcga_train_set.config b/conf/tcga_train_set.config
diff --git a/main.nf b/main.nf
@@ -28,7 +28,6 @@ params.dbsnp                = WorkflowMain.getGenomeAttribute(params, 'dbsnp')
 params.dbsnp_tbi            = WorkflowMain.getGenomeAttribute(params, 'dbsnp_tbi')
 params.known_indels         = WorkflowMain.getGenomeAttribute(params, 'known_indels')
 params.known_indels_tbi     = WorkflowMain.getGenomeAttribute(params, 'known_indels_tbi')
-params.snpeff_db            = WorkflowMain.getGenomeAttribute(params, 'snpeff_db')
 params.vep_cache_version    = WorkflowMain.getGenomeAttribute(params, 'vep_cache_version')
 params.vep_genome           = WorkflowMain.getGenomeAttribute(params, 'vep_genome')
 params.vep_species          = WorkflowMain.getGenomeAttribute(params, 'vep_species')