Merge pull request #2435 from mirpedrol/fix-subworkflows-create-name

fix subworkflow template jinja variable for subworkflow name
nf-core · Sep 25, 2023 · 54d06e8 · 54d06e8
2 parents aa7e69b + b156469
commit 54d06e8
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Showing 5 changed files with 12 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -32,6 +32,8 @@
 
 ### Subworkflows
 
+- Fix bug: missing subworkflow name when using `nf-core subworkflows create` ([#2435](https://github.com/nf-core/tools/pull/2435))
+
 ### General
 
 - Initialise `docker_image_name` to fix `UnboundLocalError` error ([#2374](https://github.com/nf-core/tools/pull/2374))

diff --git a/nf_core/subworkflow-template/subworkflows/main.nf b/nf_core/subworkflow-template/subworkflows/main.nf
@@ -7,7 +7,7 @@
 include { SAMTOOLS_SORT      } from '../../../modules/nf-core/samtools/sort/main'
 include { SAMTOOLS_INDEX     } from '../../../modules/nf-core/samtools/index/main'
 
-workflow {{ subworkflow_name|upper }} {
+workflow {{ component_name_underscore|upper }} {
 
     take:
     // TODO nf-core: edit input (take) channels

diff --git a/nf_core/subworkflow-template/subworkflows/meta.yml b/nf_core/subworkflow-template/subworkflows/meta.yml
@@ -1,5 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
-name: "{{ subworkflow_name }}"
+name: "{{ component_name_underscore }}"
 ## TODO nf-core: Add a description of the subworkflow and list keywords
 description: Sort SAM/BAM/CRAM file
 keywords:

diff --git a/nf_core/subworkflow-template/tests/main.nf b/nf_core/subworkflow-template/tests/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { {{ subworkflow_name|upper }} } from '../../../../subworkflows/{{ org }}/{{ subworkflow_dir }}/main.nf'
+include { {{ component_name_underscore|upper }} } from '../../../../subworkflows/{{ org }}/{{ subworkflow_dir }}/main.nf'
 
 workflow test_{{ component_name_underscore }} {
     {% if has_meta %}
@@ -14,5 +14,5 @@ workflow test_{{ component_name_underscore }} {
     input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
     {%- endif %}
 
-    {{ subworkflow_name|upper }} ( input )
+    {{ component_name_underscore|upper }} ( input )
 }
diff --git a/nf_core/subworkflow-template/tests/test.yml b/nf_core/subworkflow-template/tests/test.yml
@@ -1,12 +1,12 @@
 ## TODO nf-core: Please run the following command to build this file:
-#                nf-core subworkflows create-test-yml {{ subworkflow_name_underscore }}
-- name: "{{ subworkflow_name }}"
-  command: nextflow run ./tests/subworkflows/{{ org }}/{{ subworkflow_dir }} -entry test_{{ subworkflow_name }} -c ./tests/config/nextflow.config
+#                nf-core subworkflows create-test-yml {{ component_name_underscore }}
+- name: "{{ component_name_underscore }}"
+  command: nextflow run ./tests/subworkflows/{{ org }}/{{ subworkflow_dir }} -entry test_{{ component_name_underscore }} -c ./tests/config/nextflow.config
   tags:
     - "subworkflows"
-    - "subworkflows/{{ subworkflow_name }}"
+    - "subworkflows/{{ component_name_underscore }}"
   files:
-    - path: "output/{{ subworkflow_name }}/test.bam"
+    - path: "output/{{ component_name_underscore }}/test.bam"
       md5sum: e667c7caad0bc4b7ac383fd023c654fc
-    - path: output/{{ subworkflow_name }}/versions.yml
+    - path: output/{{ component_name_underscore }}/versions.yml
       md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b