Move parameters to above profiles for correct handling of params

nextflow-io · Nov 20, 2024 · 982a284 · 982a284
1 parent ecea2fe
commit 982a284
Show file tree

Hide file tree

Showing 3 changed files with 61 additions and 56 deletions.
diff --git a/hello-nextflow/hello-modules/nextflow.config b/hello-nextflow/hello-modules/nextflow.config
@@ -1,5 +1,26 @@
 docker.fixOwnership = true
 
+/*
+ * Pipeline parameters
+ */
+
+params {
+    // Primary input (file of input files, one per line)
+    reads_bam        = null
+
+    // Output directory
+    params.outdir = "results_genomics"
+
+    // Accessory files
+    reference        = null
+    reference_index  = null
+    reference_dict   = null
+    intervals        = null
+
+    // Base name for final output file
+    cohort_name      = "my_cohort"
+}
+
 profiles {
     docker_on {
         docker.enabled = true
@@ -47,21 +68,3 @@ process {
         cpus = 4
     }
 }
-
-/*
- * Pipeline parameters
- */
-
-params {
-    // Primary input (file of input files, one per line)
-    reads_bam        = null
-
-    // Accessory files
-    reference        = null
-    reference_index  = null
-    reference_dict   = null
-    intervals        = null
-
-    // Base name for final output file
-    cohort_name      = "my_cohort"
-}
diff --git a/hello-nextflow/hello-nf-test/nextflow.config b/hello-nextflow/hello-nf-test/nextflow.config
@@ -1,7 +1,25 @@
 docker.fixOwnership = true
 
-// Default output directory
-params.outdir = 'results_genomics'
+/*
+ * Pipeline parameters
+ */
+
+params {
+    // Primary input (file of input files, one per line)
+    reads_bam        = null
+
+    // Output directory
+    params.outdir = "results_genomics"
+
+    // Accessory files
+    reference        = null
+    reference_index  = null
+    reference_dict   = null
+    intervals        = null
+
+    // Base name for final output file
+    cohort_name      = "my_cohort"
+}
 
 profiles {
     docker_on {
@@ -50,21 +68,3 @@ process {
         cpus = 4
     }
 }
-
-/*
- * Pipeline parameters
- */
-
-params {
-    // Primary input (file of input files, one per line)
-    reads_bam        = null
-
-    // Accessory files
-    reference        = null
-    reference_index  = null
-    reference_dict   = null
-    intervals        = null
-
-    // Base name for final output file
-    cohort_name      = "my_cohort"
-}
diff --git a/hello-nextflow/solutions/hello-config/5-nextflow.config b/hello-nextflow/solutions/hello-config/5-nextflow.config
@@ -1,5 +1,25 @@
 docker.fixOwnership = true
 
+
+/*
+ * Pipeline parameters
+ */
+
+params {
+    // Primary input (file of input files, one per line)
+    reads_bam        = null
+
+    // Accessory files
+    reference        = null
+    reference_index  = null
+    reference_dict   = null
+    intervals        = null
+
+    // Base name for final output file
+    cohort_name      = "my_cohort"
+}
+
+
 profiles {
     docker_on {
         docker.enabled = true
@@ -44,21 +64,3 @@ process {
         cpus = 4
     }
 }
-
-/*
- * Pipeline parameters
- */
-
-params {
-    // Primary input (file of input files, one per line)
-    reads_bam        = null
-
-    // Accessory files
-    reference        = null
-    reference_index  = null
-    reference_dict   = null
-    intervals        = null
-
-    // Base name for final output file
-    cohort_name      = "my_cohort"
-}