feat: civicpy/annotate module by emmcauley · Pull Request #11079 · nf-core/modules

emmcauley · 2026-03-27T18:45:08Z

PR checklist

⚠️ This PR is contingent on some bioconda-recipe PRs that are still under review!

This module adds CIVICpy, an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase. Tests are added.

⚠️ There seems to be something wrong with the pip and conda civicpy packages, they are both lacking backports:

Traceback (most recent call last):
  File "/usr/local/bin/civicpy", line 6, in <module>
    from civicpy.cli import cli
  File "/usr/local/lib/python3.12/site-packages/civicpy/cli.py", line 4, in <module>
    from civicpy import LOCAL_CACHE_PATH, civic
  File "/usr/local/lib/python3.12/site-packages/civicpy/civic.py", line 13, in <module>
    from backports.datetime_fromisoformat import MonkeyPatch
ModuleNotFoundError: No module named 'backports.datetime_fromisoformat'

Trying to add backports into the wave container build fails even if they're both from pip.

Also logged an issue on the civicpy repo here.

emmcauley · 2026-03-27T22:26:34Z

modules/nf-core/civicpy/annotate/main.nf

+        ? 'https://depot.galaxyproject.org/singularity/civicpy:5.2.0--pyhdfd78af_0'
+        : 'docker.io/griffithlab/civicpy:v5.2.0' }"


these are non-standard because I ran into issues building the wave container for docker + singularity

We have a quay.io repository for custom docker containers. It is a recommendation to upload them there so that we stay independent of third parties that might delete the images. See the docs for more info. You can request the upload via #request-core in the nf-core slack. I think its fine to store it there until they resolve the issue on their side :)

famosab

Nice! I am also interested in having civic added to nf-core so I already added some feedback to help with the module development :)

famosab · 2026-04-13T12:27:25Z

modules/nf-core/civicpy/annotate/tests/main.nf.test

+                { assert snapshot(
+                    file(process.out.vcf[0][1]).name,
+                    process.out.versions_civicpy
+                ).match() }


You can use

{ assert snapshot(sanitizeOutput(process.out)).match() }

for the stub assertion. It should not be necessary to do any other assertions in the stub test.

famosab · 2026-04-13T12:29:10Z

modules/nf-core/civicpy/annotate/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: CIVICPY_ANNOTATE {
+        ext.args = '--include-status accepted'


We want the ext.args to be present in the main.nf.test file. That makes everything more readable in one go. See the module specifications for more info.

famosab · 2026-04-13T12:29:43Z

modules/nf-core/civicpy/annotate/main.nf

+        ? 'https://depot.galaxyproject.org/singularity/civicpy:5.2.0--pyhdfd78af_0'
+        : 'docker.io/griffithlab/civicpy:v5.2.0' }"


We have a quay.io repository for custom docker containers. It is a recommendation to upload them there so that we stay independent of third parties that might delete the images. See the docs for more info. You can request the upload via #request-core in the nf-core slack. I think its fine to store it there until they resolve the issue on their side :)

famosab · 2026-04-13T12:29:51Z

modules/nf-core/civicpy/annotate/main.nf

+    val annotation_genome_version
+
+    output:
+    tuple val(meta), path("*.vcf"),                                                                                   emit: vcf


Suggested change

tuple val(meta), path("*.vcf"), emit: vcf

tuple val(meta), path("*.vcf"), emit: vcf

famosab · 2026-04-13T12:29:56Z

modules/nf-core/civicpy/annotate/main.nf

+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}.civic"
+


Suggested change

famosab · 2026-04-13T13:07:41Z

modules/nf-core/civicpy/annotate/main.nf

+
+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}.civic"


If input and output names can overlap, use task.ext.prefix to disambiguate. For example:

if ("${vcf}" == "${prefix}.vcf.gz") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"

famosab · 2026-04-13T13:07:54Z

modules/nf-core/civicpy/annotate/main.nf

+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}.civic"
+
+    """


famosab · 2026-04-13T13:08:15Z

modules/nf-core/civicpy/annotate/meta.yml

+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "civicpy_annotate"
+
+description: A python client and analysis toolkit for the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase


Can you be more specific for annotate here?

famosab · 2026-04-13T13:11:24Z

modules/nf-core/civicpy/annotate/main.nf

+
+    civicpy annotate-vcf \\
+        --input-vcf ${vcf} \\
+        --output-vcf ${prefix}.vcf \\


We usually want the vcf files to be bgzipped if possible

famosab · 2026-04-13T13:11:46Z

modules/nf-core/civicpy/annotate/environment.yml

Conda probably has the same issue as the biocontainer / wave container?

emmcauley marked this pull request as ready for review March 27, 2026 18:46

emmcauley force-pushed the em_civipy_annotate branch 2 times, most recently from 932b1eb to ef3d2d1 Compare March 27, 2026 19:12

feat: civicpy/annotate module

249aa89

emmcauley force-pushed the em_civipy_annotate branch from ef3d2d1 to 249aa89 Compare March 27, 2026 22:26

emmcauley commented Mar 27, 2026

View reviewed changes

emmcauley marked this pull request as draft April 7, 2026 13:56

emmcauley added the new module Adding a new module label Apr 10, 2026

famosab reviewed Apr 13, 2026

View reviewed changes

		? 'https://depot.galaxyproject.org/singularity/civicpy:5.2.0--pyhdfd78af_0'
		: 'docker.io/griffithlab/civicpy:v5.2.0' }"

	tuple val(meta), path("*.vcf"), emit: vcf
	tuple val(meta), path("*.vcf"), emit: vcf

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emmcauley commented Mar 27, 2026 •

edited

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