diff --git a/CHANGELOG.md b/CHANGELOG.md index fb7bfcc991..116e55eb30 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/modules/main.nf index 83cdf90b92..404d38094d 100644 --- a/nf_core/module-template/modules/main.nf +++ b/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 + """ }