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Add stub to the modules template #2277

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merged 3 commits into from
May 5, 2023
Merged

Add stub to the modules template #2277

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affb710
Add stub to the modules template
nvnieuwk May 4, 2023
232b11d
updated changelog
nvnieuwk May 5, 2023
4d495fb
Merge branch 'dev' into add-stub-to-modules-template
jfy133 May 5, 2023
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22 changes: 22 additions & 0 deletions nf_core/module-template/modules/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
}