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Merged
ignatiusm merged 13 commits into from
Apr 8, 2025
Merged

nf-test migration: cellrangerarc/count #8008

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05a1fd7
Begin migration for cellrangerarc/count
ignatiusm Mar 24, 2025
b1fb043
Tidy up whitespace
ignatiusm Mar 25, 2025
2580631
cellrangerarc/count full test working
ignatiusm Apr 3, 2025
9bb1ab3
Merge branch 'master' into cellrangerarc/count
ignatiusm Apr 3, 2025
d72c0fe
Commiting broken stub test on purpose
ignatiusm Apr 3, 2025
762534f
Remove redundant config
ignatiusm Apr 3, 2025
0d6501d
Turn off Conda tests in CI
ignatiusm Apr 4, 2025
b49f60b
Merge branch 'master' into cellrangerarc/count
sateeshperi Apr 7, 2025
84a8b20
Merge branch 'master' into cellrangerarc/count
ignatiusm Apr 8, 2025
5cde2e8
Add nextflow.config
ignatiusm Apr 8, 2025
39b7f4c
Add single whitespace to add this file to CI tests
ignatiusm Apr 8, 2025
f65f635
Revert "Add single whitespace to add this file to CI tests"
ignatiusm Apr 8, 2025
96b16e4
Revert "Revert "Add single whitespace to add this file to CI tests""
ignatiusm Apr 8, 2025
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1 change: 1 addition & 0 deletions .github/skip_nf_test.json
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Expand Up @@ -18,6 +18,7 @@
"modules/nf-core/cellranger/mkvdjref",
"modules/nf-core/cellranger/multi",
"modules/nf-core/cellranger/vdj",
"modules/nf-core/cellrangerarc/count",
"modules/nf-core/cellrangerarc/mkgtf",
"modules/nf-core/checkqc",
"modules/nf-core/coreograph",
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2 changes: 0 additions & 2 deletions .github/workflows/pytest-workflow.yml
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Expand Up @@ -100,8 +100,6 @@ jobs:
tags: bwa/samse
- profile: conda
tags: cellpose
- profile: conda
tags: cellrangerarc/count
- profile: conda
tags: cellrangerarc/mkfastq
- profile: conda
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171 changes: 171 additions & 0 deletions modules/nf-core/cellrangerarc/count/tests/main.nf.test
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@@ -0,0 +1,171 @@
nextflow_process {

name "Test Process CELLRANGERARC_COUNT"
script "../main.nf"
process "CELLRANGERARC_COUNT"

tag "modules"
tag "modules_nfcore"
tag "cellrangerarc"
tag "cellrangerarc/mkref"
tag "cellrangerarc/count"
tag "unzip"

setup {
run("UNZIP") {
script "../../../unzip/main.nf"

process {
"""
input[0] = [[],file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.fa.gz',checkIfExists:true)]
"""
}
}
run("CELLRANGERARC_MKREF") {
script "../../mkref/main.nf"

process {
"""
input[0] = UNZIP.out.unzipped_archive.map{it[1]}+"/chr19.fa"
input[1] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/genome/chr19.filtered.gtf.gz',checkIfExists:true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome_motifs.txt',checkIfExists:true)
input[3] = file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/cellranger_arc_mkref_test_mm39_chr19_config.json',checkIfExists:true)
input[4] = "cellrangerarc_reference"
"""
}
}
}
test("test_cellrangerarc_count") {

when {
params {
module_args = ''
}
process {
"""
input[0] = [[id:'test'],['gex','atac'],['SRR18907480_chr19_sub','SRR18907481_chr19_sub'],
[file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R1_001.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907480_chr19_sub_S1_L001_R2_001.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R1_001.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_R2_001.fastq.gz',checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/mus_musculus/illumina/10xgenomics/multiome/SRR18907481_chr19_sub_S1_L001_I2_001.fastq.gz',checkIfExists:true)
]
]
input[1] = CELLRANGERARC_MKREF.out.reference
"""
}
}
then {
assertAll(
{ assert process.success },
{
def all_files = process.out.outs[0][1]

def stable_file_names = [
'analysis/clustering/atac/graphclust/clusters.csv',
'analysis/clustering/atac/graphclust/differential_accessibility.csv',
'analysis/clustering/atac/graphclust/differential_expression.csv',
'analysis/clustering/atac/kmeans_2_clusters/clusters.csv',
'analysis/clustering/atac/kmeans_2_clusters/differential_accessibility.csv',
'analysis/clustering/atac/kmeans_2_clusters/differential_expression.csv',
'analysis/clustering/atac/kmeans_3_clusters/clusters.csv',
'analysis/clustering/atac/kmeans_3_clusters/differential_accessibility.csv',
'analysis/clustering/atac/kmeans_3_clusters/differential_expression.csv',
'analysis/clustering/atac/kmeans_4_clusters/clusters.csv',
'analysis/clustering/atac/kmeans_4_clusters/differential_accessibility.csv',
'analysis/clustering/atac/kmeans_4_clusters/differential_expression.csv',
'analysis/clustering/atac/kmeans_5_clusters/clusters.csv',
'analysis/clustering/atac/kmeans_5_clusters/differential_accessibility.csv',
'analysis/clustering/atac/kmeans_5_clusters/differential_expression.csv',
'analysis/clustering/gex/graphclust/clusters.csv',
'analysis/clustering/gex/graphclust/differential_accessibility.csv',
'analysis/clustering/gex/graphclust/differential_expression.csv',
'analysis/clustering/gex/kmeans_2_clusters/clusters.csv',
'analysis/clustering/gex/kmeans_2_clusters/differential_accessibility.csv',
'analysis/clustering/gex/kmeans_2_clusters/differential_expression.csv',
'analysis/clustering/gex/kmeans_3_clusters/clusters.csv',
'analysis/clustering/gex/kmeans_3_clusters/differential_accessibility.csv',
'analysis/clustering/gex/kmeans_3_clusters/differential_expression.csv',
'analysis/clustering/gex/kmeans_4_clusters/clusters.csv',
'analysis/clustering/gex/kmeans_4_clusters/differential_accessibility.csv',
'analysis/clustering/gex/kmeans_4_clusters/differential_expression.csv',
'analysis/clustering/gex/kmeans_5_clusters/clusters.csv',
'analysis/clustering/gex/kmeans_5_clusters/differential_accessibility.csv',
'analysis/clustering/gex/kmeans_5_clusters/differential_expression.csv',
'analysis/dimensionality_reduction/atac/lsa_components.csv',
'analysis/dimensionality_reduction/atac/lsa_dispersion.csv',
'analysis/dimensionality_reduction/atac/lsa_features_selected.csv',
'analysis/dimensionality_reduction/atac/lsa_projection.csv',
'analysis/dimensionality_reduction/atac/lsa_variance.csv',
'analysis/dimensionality_reduction/atac/tsne_projection.csv',
'analysis/dimensionality_reduction/atac/umap_projection.csv',
'analysis/dimensionality_reduction/gex/pca_components.csv',
'analysis/dimensionality_reduction/gex/pca_dispersion.csv',
'analysis/dimensionality_reduction/gex/pca_features_selected.csv',
'analysis/dimensionality_reduction/gex/pca_projection.csv',
'analysis/dimensionality_reduction/gex/pca_variance.csv',
'analysis/dimensionality_reduction/gex/tsne_projection.csv',
'analysis/dimensionality_reduction/gex/umap_projection.csv',
'analysis/feature_linkage/feature_linkage.bedpe',
'analysis/tf_analysis/filtered_tf_bc_matrix/barcodes.tsv.gz',
'analysis/tf_analysis/filtered_tf_bc_matrix/matrix.mtx.gz',
'analysis/tf_analysis/filtered_tf_bc_matrix/motifs.tsv',
'analysis/tf_analysis/peak_motif_mapping.bed',
'atac_cut_sites.bigwig',
'atac_peak_annotation.tsv',
'filtered_feature_bc_matrix/barcodes.tsv.gz',
'filtered_feature_bc_matrix/features.tsv.gz',
'filtered_feature_bc_matrix/matrix.mtx.gz',
'gex_molecule_info.h5',
'gex_possorted_bam.bam',
'gex_possorted_bam.bam.bai',
'per_barcode_metrics.csv',
'raw_feature_bc_matrix/barcodes.tsv.gz',
'raw_feature_bc_matrix/features.tsv.gz',
'raw_feature_bc_matrix/matrix.mtx.gz',
'summary.csv',
]

def stable_files = all_files.findAll { file ->
// Check if the file path ends with any of the stable file paths
return stable_file_names.any { stable_path ->
file.toString().endsWith(stable_path)
}
}.toSorted()

assert snapshot(
stable_files,
process.out.versions[0]
).match()

def unstable_file_names = [
'analysis/feature_linkage/feature_linkage_matrix.h5',
'analysis/tf_analysis/filtered_tf_bc_matrix.h5',
'atac_fragments.tsv.gz',
'atac_fragments.tsv.gz.tbi',
'atac_peaks.bed',
'atac_possorted_bam.bam',
'atac_possorted_bam.bam.bai',
'cloupe.cloupe',
'filtered_feature_bc_matrix.h5',
'raw_feature_bc_matrix.h5',
'web_summary.html'
]

def unstable_files = all_files.findAll { file ->
return unstable_file_names.any { unstable_path ->
file.toString().endsWith(unstable_path)
}
}.toSorted()

unstable_files.each { filePath ->
def fileObj = file(filePath)
assert fileObj.exists(): "File ${filePath} does not exist"
}
}
)
}
}
// No stub test, as the stub test for `UNZIP` doesn't actually extract the archive.
// This breaks the downstream stub tests as a fasta file is required.
}
76 changes: 76 additions & 0 deletions modules/nf-core/cellrangerarc/count/tests/main.nf.test.snap
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{
"test_cellrangerarc_count": {
"content": [
[
"clusters.csv:md5,ed29b219ca3b79305129aea2d38ca60e",
"differential_accessibility.csv:md5,90e3e1001432bd1f94f53f39ae86971c",
"differential_expression.csv:md5,2806595b0c66af8407977b6ea57e30a3",
"clusters.csv:md5,35232075d0184cc6a31178ed58176bbe",
"differential_accessibility.csv:md5,0c597e33c58aac61a54e71c0ca3d1343",
"differential_expression.csv:md5,e77580db30873fba52bf4490f752ed22",
"clusters.csv:md5,127636548ad77bfa2646cbf62209e73b",
"differential_accessibility.csv:md5,9d1efbb7209c95a6f7714b43aca22130",
"differential_expression.csv:md5,24a85767ec0013a9f444bed5b23fb7f2",
"clusters.csv:md5,c84df7cc5cb684dd4a431915df0b58b2",
"differential_accessibility.csv:md5,2492068224aba9a65f860b6fb3464056",
"differential_expression.csv:md5,e02a8c8e3bc1d924357b46af2da76a6b",
"clusters.csv:md5,fcbbc4f29456778935fbbf4dc52791ea",
"differential_accessibility.csv:md5,630f412020f85765b2a32ac689701ce5",
"differential_expression.csv:md5,0aae96dbf649f0bc738f5d2c19e2be76",
"clusters.csv:md5,6cd4c2b06047c99cee59548c9b3000ac",
"differential_accessibility.csv:md5,08fc89ad11d1834cab677390f385a88a",
"differential_expression.csv:md5,6e97ced39f84b02f843f0b757b02f100",
"clusters.csv:md5,cd135bf9e9b5aa69abe95d5356aec96c",
"differential_accessibility.csv:md5,9ef66432c3f66f2190ff936324091e9f",
"differential_expression.csv:md5,223e516ce7ddf219575a32a60217e83d",
"clusters.csv:md5,ae9c24a834f1863a8faf03b3b4bdf74a",
"differential_accessibility.csv:md5,84bf1b3b3c90abdd92a817cc5a9d2ee8",
"differential_expression.csv:md5,8b0ec69f3cd0d3156d6def50cdde4340",
"clusters.csv:md5,aceb697994f98ee50b4d3db8e12e2a3a",
"differential_accessibility.csv:md5,05f0b3a10ce71d2fbafc6c9b74acf969",
"differential_expression.csv:md5,7b339771b1731b9cff2c52ac4fc632ce",
"clusters.csv:md5,243233d51193e6ce3127ed5ef8a08daf",
"differential_accessibility.csv:md5,25deefdff4c870e52c84f97cc4b9d5d2",
"differential_expression.csv:md5,b70730d7301cba11c46297d08b81677d",
"lsa_components.csv:md5,c3a48d3849f6b5e268bcb16b4d3db7ec",
"lsa_dispersion.csv:md5,1bdae634bd63d044dcfd8ae821b3744c",
"lsa_features_selected.csv:md5,b4e3cc5cac26dc6df059c1b8e38e72a8",
"lsa_projection.csv:md5,3bce47a5a0e8dc0cb24c2ecbba5c745b",
"lsa_variance.csv:md5,ff92c64ec140084673fd7ec48ce48993",
"tsne_projection.csv:md5,b0ff0a327a7cad898087c169b9815bab",
"umap_projection.csv:md5,8a34ad7bcf4ae7d14ad8f451acb4a12e",
"pca_components.csv:md5,82a4384a22390821cbfe06b2de9e9b4d",
"pca_dispersion.csv:md5,a6c8d15062a67bf828c1b58d1bc1eff8",
"pca_features_selected.csv:md5,34acd3e8d57f68bf592856c0c69847e7",
"pca_projection.csv:md5,6a2bf5e268da6705b92ec02309b3f61e",
"pca_variance.csv:md5,060e80415e690a7bfc9cd385c929842f",
"tsne_projection.csv:md5,aa42abe3c868c7d0e35628acf1a24966",
"umap_projection.csv:md5,34acdb54ff9f9c8b7d7f91a625450294",
"feature_linkage.bedpe:md5,4a92b2e49591c21a3d08602235e6ef7a",
"barcodes.tsv.gz:md5,1b2010b38c2de59bea1b71d374114919",
"matrix.mtx.gz:md5,2627809b0951961282c3b31fb83d7f1b",
"motifs.tsv:md5,9a397341713d07560937054df442afcb",
"peak_motif_mapping.bed:md5,b1d02a287485989ca294284bd95ad572",
"atac_cut_sites.bigwig:md5,03e0c63674192256d55a3c117fff66ee",
"atac_peak_annotation.tsv:md5,f4770b4197ff32c74bd206476f1f0dba",
"barcodes.tsv.gz:md5,1b2010b38c2de59bea1b71d374114919",
"features.tsv.gz:md5,9a315f46dbf99b9120527df78fd7e081",
"matrix.mtx.gz:md5,2304085aaac98027cf9241a3b2593760",
"gex_molecule_info.h5:md5,f1ab414eb8b8da017c974d7109f5e7ca",
"gex_possorted_bam.bam:md5,8455846fa1aa417e4252bd09584d1098",
"gex_possorted_bam.bam.bai:md5,444fb175b75d0e22c8e14724b7790e34",
"per_barcode_metrics.csv:md5,055ddb433b94d44efa0113a1db84a63d",
"barcodes.tsv.gz:md5,4e020c4c968100a61a542c0d6e56e5f5",
"features.tsv.gz:md5,9a315f46dbf99b9120527df78fd7e081",
"matrix.mtx.gz:md5,743fc9d85f85cd2e5a40654d3ae2e3e4",
"summary.csv:md5,7641192d4cc0c6072dc447a46d5f89a2"
],
"versions.yml:md5,dc627e4bae7ded9a34b7e8f52b4b903d"
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
},
"timestamp": "2025-04-03T18:30:31.250399555"
}
}
5 changes: 0 additions & 5 deletions tests/config/pytest_modules.yml
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@@ -1,8 +1,3 @@
cellrangerarc/count:
- modules/nf-core/cellrangerarc/count/**
- tests/modules/nf-core/cellrangerarc/count/**
- modules/nf-core/cellrangerarc/mkref/**
- tests/modules/nf-core/cellrangerarc/mkref/**
cellrangerarc/mkfastq:
- modules/nf-core/cellrangerarc/mkfastq/**
- tests/modules/nf-core/cellrangerarc/mkfastq/**
Expand Down
39 changes: 0 additions & 39 deletions tests/modules/nf-core/cellrangerarc/count/main.nf
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27 changes: 0 additions & 27 deletions tests/modules/nf-core/cellrangerarc/count/nextflow.config
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