add gcta/gsmr tool by juliaapolonio · Pull Request #8140 · nf-core/modules

juliaapolonio · 2025-03-26T20:08:00Z

PR checklist

Closes #7975

juliaapolonio · 2025-03-26T20:18:08Z

Hi, I'm having linting issues with my code, in the meta.yml file. The error message is " The meta.yml of the module gcta/gsmr is not valid: {'reference': {'type': 'file', 'description': 'Reference files (BED, BIM, FAM) for GCTA analysis', 'pattern': '*.{bed,bim,fam}', multiple': True}} is not of type 'array'. Check the entry for input. "
I wasn't able to figure this out...

d4straub

Looks good, but args seem quite important to me.

famosab · 2025-03-31T11:27:56Z

+            assert snapshot(
+                process.out.gsmr,
+                process.out.eff_plot,
+                process.out.mono_badsnps,
+                process.out.versions
+            ).match()
+            assert path(process.out.versions.get(0)).text.contains("GSMR")


Suggested change

assert snapshot(

process.out.gsmr,

process.out.eff_plot,

process.out.mono_badsnps,

process.out.versions

).match()

assert path(process.out.versions.get(0)).text.contains("GSMR")

assert snapshot(process.out).match()

That should work or is the md5sum of the log instable?

Yes the log is instable.

ok then still this line is not neceassry :)
assert path(process.out.versions.get(0)).text.contains("GSMR")

famosab · 2025-03-31T11:28:57Z

+                "test_exposure_test_outcome.gsmr:md5,f137c763773522ea37849d919f6de9aa"
+            ],
+            [
+


Is it expected that there is no eff_plot?

Yes, gsmr only emits the eff_plot when there are significant IVs which is not the case for this test data.

famosab · 2025-03-31T11:30:42Z

+    path "${meta.id}_${meta2.id}.log"         , emit: log
+    path "${meta.id}_${meta2.id}.gsmr"        , emit: gsmr
+    path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true
+    path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true


Suggested change

path "${meta.id}_${meta2.id}.log" , emit: log

path "${meta.id}_${meta2.id}.gsmr" , emit: gsmr

path "${meta.id}_${meta2.id}.eff_plot.gz" , emit: eff_plot, optional: true

path "${meta.id}_${meta2.id}.mono.badsnps", emit: mono_badsnps, optional: true

path "*.log" , emit: log

path "*.gsmr" , emit: gsmr

path "*.eff_plot.gz" , emit: eff_plot, optional: true

path "*.mono.badsnps", emit: mono_badsnps, optional: true

These need to be generic so that the pipeline dev can in therory change the prefix :)

That's true! But when I remove these {meta}, the lint fails with this message: 'meta' map not emitted in output channel(s)
Do you know a workaround for this?

Ah its because you do not emit the meta map :) the output needs to be structured as tuples:

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

and so on :)

Thanks for the help! I added this modification in my last commit

I think we allow only one meta map per output. Maybe you can ask in the slack for help for your specific use-case.

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

* master: (1721 commits) Remove non-standard ext keys to comply with nf-core guidelines (nf-core#10806) Migrate bam2fastx/bam2fastq module to topic channels (nf-core#10438) Remove ext.batch_size to comply with nf-core guidelines (nf-core#10655) Add an input channel to `blast/makeblastedb` for taxonomic information. (nf-core#10802) Move ext.postprocessing script to input to comply with nf-core guidelines (nf-core#10819) Update to topics `eido/*` (nf-core#10881) Remove ext.metrics to comply with nf-core guidelines (nf-core#10900) Ensure fastq_list is always a list in `generateReadgroupBCLCONVERT` function (nf-core#10901) Remove ext.context_type to conform to nf-core guidelines (nf-core#10442) Update to topics `crisprcleanr/normalize` (nf-core#10828) Migrate Diann versions to topic (nf-core#10883) feat(stardist): update to Seqera Containers GPU image with model input (nf-core#10332) Add SVIM module (nf-core#10350) samtools merge - single index output (nf-core#10898) Rattle cluster (nf-core#7447) Adding a log to record stdout from Genescopefk (nf-core#10897) This pr closes nf-core#10757 (nf-core#10871) 10657 migration to topics channels cnvpytorhistogram (nf-core#10870) 10660 migration to topics channels cnvpytorview (nf-core#10874) esearch migration to topics (nf-core#10887) ...

famosab · 2026-04-08T14:19:30Z

Might be replaced by #10995?

juliaapolonio · 2026-04-08T19:41:05Z

Might be replaced by #10995?

No, it's the same tool but different functions (#10995 is --make-grm and #8140 is gsmr)

famosab

Just some minor things and then we can get this merged :)

famosab · 2026-04-09T07:10:01Z

+                { assert process.success },
+                { assert snapshot(process.out.gsmr).match("gsmr_stub")},
+                { assert snapshot(process.out.versions_gcta).match("versions_gcta_stub")}
+            )


see above commenz

famosab · 2026-04-09T07:10:10Z

You can run

nextflow lint -format -sort-declarations -spaces 4 -harshil-alignment

on this file to clean this up nicely.

SPPearce · 2026-05-18T12:47:08Z

Bump for @juliaapolonio , shall we get this finished off?

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

SPPearce · 2026-05-24T16:07:39Z

+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gcta:1.94.1--h9ee0642_0':
+        'biocontainers/gcta:1.94.1--h9ee0642_0' }"


Suggested change

'biocontainers/gcta:1.94.1--h9ee0642_0' }"

'quay.io/biocontainers/gcta:1.94.1--h9ee0642_0' }"

SPPearce · 2026-05-24T16:08:13Z

+    def prefix = task.ext.prefix ?: "${meta.id}_${meta2.id}"
+    """
+    echo "${meta.id} ${exposure}" > ${meta.id}.input.txt
+    echo "${meta2.id} ${outcome}" > ${meta2.id} .outcome.txt


Suggested change

echo "${meta2.id} ${outcome}" > ${meta2.id} .outcome.txt

echo "${meta2.id} ${outcome}" > ${meta2.id}.outcome.txt

SPPearce · 2026-05-24T16:09:42Z

+                """
+                input[0] = [
+                    [ id:'test_exposure' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")


Can you swap to using the modules_testdata_base_path like this:

Suggested change

file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")

file(params.modules_testdata_base_path + "genomics/homo_sapiens/gsmr/sumstats.tsv")

SPPearce · 2026-05-24T16:11:31Z

+                { assert snapshot(process.out.gsmr).match("gsmr")},
+                { assert snapshot(process.out.versions_gcta).match("versions_gcta")}
+                { assert snapshot(
+                    process.out.gsmr,
+                    process.out.versions_gcta
+                    ).match("versions_gcta")}


Suggested change

{ assert snapshot(process.out.gsmr).match("gsmr")},

{ assert snapshot(process.out.versions_gcta).match("versions_gcta")}

{ assert snapshot(

process.out.gsmr,

process.out.versions_gcta

).match("versions_gcta")}

{ assert snapshot(sanitizeOutput(process.out, unstableKeys:["log"]).match()}

add gcta/gsmr tool

b5da922

juliaapolonio added 6 commits March 27, 2025 08:05

solve part of linting issues

179a1b3

fix identation of meta.yml

acab75f

fix all linting issues

ed69765

remove unecessary file

6b09431

fix prefix definition

662c582

fix harshil alignment

5f3af7c

d4straub reviewed Mar 27, 2025

View reviewed changes

Comment thread modules/nf-core/gcta/gsmr/main.nf Outdated

Comment thread modules/nf-core/gcta/gsmr/main.nf Outdated

Comment thread modules/nf-core/gcta/gsmr/main.nf Outdated

Comment thread modules/nf-core/gcta/gsmr/main.nf

famosab reviewed Mar 31, 2025

View reviewed changes

juliaapolonio and others added 3 commits April 3, 2025 09:18

address daniel suggestions

5d734e0

Apply suggestions from code review

fff21d8

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

fix linting

dacd852

juliaapolonio requested a review from d4straub April 3, 2025 12:47

juliaapolonio added 6 commits April 3, 2025 09:51

delete unnecessary files

a8d926f

fix one linting issue

8ee1083

change meta.yml according to main

0431c2b

forgot to add meta.yml

1086cef

Merge branch 'master' into gcta_gsmr

47d989b

change output format to tuple

7755b75

atrigila added the awaiting-changes will be closed after 30 days label Mar 5, 2026

juliaapolonio and others added 5 commits March 13, 2026 16:20

migrate to topics; fix linting and nf-test

3448573

make module pass pre-commit

d274b21

fix: Linting & obsolete snap

6fd2487

fix: Remove linebreak

943d57e

jvfe added Ready for Review and removed awaiting-changes will be closed after 30 days labels Mar 14, 2026

Merge branch 'master' into gcta_gsmr

2889cc9

famosab mentioned this pull request Apr 8, 2026

Add gcta/addgrms module #10995

Open

14 tasks

famosab reviewed Apr 9, 2026

View reviewed changes

juliaapolonio and others added 2 commits May 20, 2026 12:23

Apply suggestions from code review

97e85f9

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>

Merge branch 'master' into gcta_gsmr

27af6ce

SPPearce requested changes May 24, 2026

View reviewed changes

	'biocontainers/gcta:1.94.1--h9ee0642_0' }"
	'quay.io/biocontainers/gcta:1.94.1--h9ee0642_0' }"

	echo "${meta2.id} ${outcome}" > ${meta2.id} .outcome.txt
	echo "${meta2.id} ${outcome}" > ${meta2.id}.outcome.txt

	file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/gsmr/sumstats.tsv")
	file(params.modules_testdata_base_path + "genomics/homo_sapiens/gsmr/sumstats.tsv")

Conversation

juliaapolonio commented Mar 26, 2025

PR checklist

Uh oh!

juliaapolonio commented Mar 26, 2025

Uh oh!

d4straub left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

famosab commented Apr 8, 2026

Uh oh!

juliaapolonio commented Apr 8, 2026

Uh oh!

famosab left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

SPPearce commented May 18, 2026

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

6 participants