Merge pull request #2277 from nvnieuwk/add-stub-to-modules-template

Add stub to the modules template

CHANGELOG.md

@@ -6,6 +6,7 @@
 
 - Remove `cleanup = true` from `test_full.config` in pipeline template
 - Fix usage docs for specifying `params.yaml`
+- Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk]
 
 ### Linting
 

nf_core/module-template/modules/main.nf

@@ -94,4 +94,26 @@ process {{ component_name_underscore|upper }} {
         {{ tool }}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    {% if has_meta -%}
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    {%- endif %}
+    {% if not_empty_template -%}
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    {%- endif %}
+    """
+    {% if not_empty_template -%}
+    touch ${prefix}.bam
+    {%- endif %}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        {{ tool }}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }