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Update decoupler #7068

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Update decoupler #7068

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2b3c444
chore(#6134): Move environment file
edmundmiller Nov 22, 2024
5368961
chore: Remove ='s in container
edmundmiller Nov 22, 2024
2f1259b
chore: Manually bump version
edmundmiller Nov 22, 2024
4f11c0c
test: Output version
edmundmiller Nov 22, 2024
9e7ea93
style: Run lsp format
edmundmiller Nov 22, 2024
3a3573b
build: Use Seqera containers
edmundmiller Nov 22, 2024
c935590
fix: Update version to file
edmundmiller Nov 22, 2024
f9e5dd1
Updated test data paths and added a stub
GallVp Nov 24, 2024
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8 changes: 8 additions & 0 deletions modules/nf-core/decoupler/decoupler/environment.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
- conda-forge
- bioconda
dependencies:
# renovate: datasource=conda depName=conda-forge/decoupler-py
- conda-forge::decoupler-py=1.8.0
38 changes: 29 additions & 9 deletions modules/nf-core/decoupler/decoupler/main.nf
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Original file line number Diff line number Diff line change
@@ -1,18 +1,19 @@
process DECOUPLER {
tag "$meta.id"
tag "${meta.id}"
label 'process_medium'

conda "conda-forge::decoupler-py=1.6.0"
container = "ghcr.io/saezlab/publish-packages/decoupler:sha-5838309"
conda "${moduleDir}/environment.yml"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/cf/cf3578c5f4a5ad40d10b535d496daa29f47e908fbbbc789f85e3341b8f9341ba/data'
: 'community.wave.seqera.io/library/decoupler-py:1.8.0--b139c6574c0ac2a6'}"

input:
tuple val(meta), path(mat)
path(net)
path net

output:
tuple val(meta), path("*estimate__decoupler.tsv"), emit: dc_estimate
tuple val(meta), path("*pvals__decoupler.tsv"), emit: dc_pvals
path("versions.yml"), emit: versions
tuple val(meta), path("*estimate__decoupler.tsv") , emit: dc_estimate
tuple val(meta), path("*pvals__decoupler.tsv") , emit: dc_pvals
path("versions.yml") , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -66,6 +67,25 @@ process DECOUPLER {
## VERSIONS FILE
with open('versions.yml', 'a') as version_file:
version_file.write('"${task.process}":' + "\\n")
version_file.write("\tdecoupler-py: " + dc.__version__ + "\\n")
version_file.write(f" decoupler-py: {dc.__version__}\\n")
"""

stub:
"""
#!/usr/bin/env python3
import decoupler as dc

## dc_estimate
with open('consensus_estimate__decoupler.tsv', 'a') as tsv_file:
tsv_file.write('')

## dc_pvals
with open('consensus_pvals__decoupler.tsv', 'a') as tsv_file:
tsv_file.write('')

## VERSIONS FILE
with open('versions.yml', 'a') as version_file:
version_file.write('"${task.process}":' + "\\n")
version_file.write(f" decoupler-py: {dc.__version__}\\n")
"""
}
34 changes: 31 additions & 3 deletions modules/nf-core/decoupler/decoupler/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -17,10 +17,38 @@ nextflow_process {
"""
input[0] = [
[ id: 'test' ],
file(params.test_data['generic']['tsv']['expression'], checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true)
]
input[1] = [
file(params.test_data['generic']['tsv']['network'], checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true)
]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") },
)
}

}

test("decoupler_test - stub") {

options '-stub'

when {
process {
"""
input[0] = [
[ id: 'test' ],
file(params.modules_testdata_base_path + 'generic/tsv/expression.tsv', checkIfExists: true)
]
input[1] = [
file(params.modules_testdata_base_path + 'generic/tsv/network.tsv', checkIfExists: true)
]
"""
}
Expand All @@ -35,4 +63,4 @@ nextflow_process {

}

}
}
101 changes: 82 additions & 19 deletions modules/nf-core/decoupler/decoupler/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,4 +1,67 @@
{
"decoupler_test - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"consensus_estimate__decoupler.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test"
},
"consensus_pvals__decoupler.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,8fd115b4099050429b348981ca1d5e86"
],
"dc_estimate": [
[
{
"id": "test"
},
"consensus_estimate__decoupler.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"dc_pvals": [
[
{
"id": "test"
},
"consensus_pvals__decoupler.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,8fd115b4099050429b348981ca1d5e86"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-25T11:03:58.583432"
},
"versions": {
"content": [
{
"DECOUPLER": {
"decoupler-py": "1.8.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-11-22T15:53:36.673249"
},
"decoupler_test": {
"content": [
{
Expand All @@ -8,10 +71,10 @@
"id": "test"
},
[
"consensus_estimate__decoupler.tsv:md5,f762d3282a81c61b127e97d044e9ddd7",
"mlm_estimate__decoupler.tsv:md5,ce7ce3c710fe188035b6706512ffbf54",
"ulm_estimate__decoupler.tsv:md5,14773953134037a208fe3c95c893acae",
"wsum_estimate__decoupler.tsv:md5,2488716cfe85c1306cb76cf117808d97"
"consensus_estimate__decoupler.tsv:md5,3adfc527d7491baaec5a9ba003345b06",
"mlm_estimate__decoupler.tsv:md5,10f0a0a82dc252e2843df04430daa30c",
"ulm_estimate__decoupler.tsv:md5,3f38c1f33d6fdf352bc311e269662c79",
"wsum_estimate__decoupler.tsv:md5,5e6c68334b105b341042507638e3a950"
]
]
],
Expand All @@ -21,26 +84,26 @@
"id": "test"
},
[
"consensus_pvals__decoupler.tsv:md5,35850081a4308deba35d171a266bedd0",
"mlm_pvals__decoupler.tsv:md5,016a15c3dcf688fcdf3ccbd40e06d64f",
"ulm_pvals__decoupler.tsv:md5,531a3ed641bf3c1b0b105cfaee5864cd",
"consensus_pvals__decoupler.tsv:md5,01b956e8cd0c0f24858c83382792f3ba",
"mlm_pvals__decoupler.tsv:md5,70e53ea27d51f0b74de08e09cfa0d22a",
"ulm_pvals__decoupler.tsv:md5,024d29e68941f56d4f2e878826ad4ded",
"wsum_pvals__decoupler.tsv:md5,fac9e18b9495ca8a9ae92a015eed3043"
]
]
],
"2": [
"versions.yml:md5,01a24ec9e3499a0d2f54e7fb173537be"
"versions.yml:md5,8fd115b4099050429b348981ca1d5e86"
],
"dc_estimate": [
[
{
"id": "test"
},
[
"consensus_estimate__decoupler.tsv:md5,f762d3282a81c61b127e97d044e9ddd7",
"mlm_estimate__decoupler.tsv:md5,ce7ce3c710fe188035b6706512ffbf54",
"ulm_estimate__decoupler.tsv:md5,14773953134037a208fe3c95c893acae",
"wsum_estimate__decoupler.tsv:md5,2488716cfe85c1306cb76cf117808d97"
"consensus_estimate__decoupler.tsv:md5,3adfc527d7491baaec5a9ba003345b06",
"mlm_estimate__decoupler.tsv:md5,10f0a0a82dc252e2843df04430daa30c",
"ulm_estimate__decoupler.tsv:md5,3f38c1f33d6fdf352bc311e269662c79",
"wsum_estimate__decoupler.tsv:md5,5e6c68334b105b341042507638e3a950"
]
]
],
Expand All @@ -50,22 +113,22 @@
"id": "test"
},
[
"consensus_pvals__decoupler.tsv:md5,35850081a4308deba35d171a266bedd0",
"mlm_pvals__decoupler.tsv:md5,016a15c3dcf688fcdf3ccbd40e06d64f",
"ulm_pvals__decoupler.tsv:md5,531a3ed641bf3c1b0b105cfaee5864cd",
"consensus_pvals__decoupler.tsv:md5,01b956e8cd0c0f24858c83382792f3ba",
"mlm_pvals__decoupler.tsv:md5,70e53ea27d51f0b74de08e09cfa0d22a",
"ulm_pvals__decoupler.tsv:md5,024d29e68941f56d4f2e878826ad4ded",
"wsum_pvals__decoupler.tsv:md5,fac9e18b9495ca8a9ae92a015eed3043"
]
]
],
"versions": [
"versions.yml:md5,01a24ec9e3499a0d2f54e7fb173537be"
"versions.yml:md5,8fd115b4099050429b348981ca1d5e86"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.1"
},
"timestamp": "2024-03-21T15:58:23.677564728"
"timestamp": "2024-11-22T15:53:36.587951"
}
}
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