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Bump star version and port tests to nf-test #5529

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Bump star version and port tests to nf-test #5529

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8f1f908
bump STAR, drop mulled container, fix tests
matthdsm Apr 26, 2024
088a73f
Merge branch 'master' into bump/star
matthdsm Apr 26, 2024
af9ba09
prettier
matthdsm Apr 26, 2024
c737eb5
linting
matthdsm Apr 26, 2024
981bee7
fix arriba tests
matthdsm Apr 29, 2024
85e7439
arriba: fix permission denied error
matthdsm Apr 29, 2024
8d39589
try to fix tests
matthdsm Apr 29, 2024
d0e0a57
Update modules/nf-core/arriba/arriba/tests/main.nf.test
matthdsm Apr 29, 2024
b20114d
update star/align test
nvnieuwk May 23, 2024
d59c42e
update star/genomegenerate snap
nvnieuwk May 23, 2024
746c395
Merge branch 'master' into bump/star
nvnieuwk May 23, 2024
a84f0f5
fix fastq_align_dna snap
nvnieuwk May 23, 2024
cde4715
update genomegenerate container to seqera container
nvnieuwk May 23, 2024
b34ef1c
retry star with another container
nvnieuwk May 23, 2024
b400a3f
reintroduce mulled
nvnieuwk May 24, 2024
608f8ea
fix fastq_align_star tests
nvnieuwk May 24, 2024
659b970
fix star/align tests
nvnieuwk May 27, 2024
d90349b
comment out the docker options
nvnieuwk May 27, 2024
7b38fa6
Merge branch 'master' into bump/star
nvnieuwk May 27, 2024
a4e8cfd
add docker run options to all failing tests
nvnieuwk May 27, 2024
f074c2f
Merge branch 'bump/star' of https://github.com/nf-core/modules into b…
nvnieuwk May 27, 2024
e5035bd
test adding config to setup
nvnieuwk May 27, 2024
4aec437
add forgotten docker run options
nvnieuwk May 27, 2024
0eb1be0
let's see what this does
nvnieuwk May 27, 2024
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207 changes: 207 additions & 0 deletions modules/nf-core/arriba/arriba/tests/main.nf.test
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nextflow_process {

name "Test Process ARRIBA_ARRIBA"
script "../main.nf"
config "./nextflow.config"
process "ARRIBA_ARRIBA"

tag "modules"
tag "modules_nfcore"
tag "arriba"
tag "arriba/arriba"
tag "star"
tag "star/align"
tag "star/genomegenerate"

setup {
run("STAR_GENOMEGENERATE") {
script "../../../star/genomegenerate/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
input[1] = Channel.of([
[ id:'test_fai' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
])
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
"""
}
}
}

test("homo_sapiens - single_end") {
setup {
run("STAR_ALIGN") {
script "../../../star/align/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:true ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
input[5] = false
"""
}
}
}

when {
process {
"""
input[0] = STAR_ALIGN.out.bam
input[1] = Channel.of([
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [[],[]]
input[7] = [[],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("homo_sapiens - paired_end") {
setup {
run("STAR_ALIGN") {
script "../../../star/align/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
input[5] = false
"""
}
}
}

when {
process {
"""
input[0] = STAR_ALIGN.out.bam
input[1] = Channel.of([
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [[],[]]
input[7] = [[],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("homo_sapiens - paired_end - stub") {

options "-stub"

setup {
run("STAR_ALIGN") {
script "../../../star/align/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true)
]
])
input[1] = STAR_GENOMEGENERATE.out.index
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = false
input[4] = 'illumina'
input[5] = false
"""
}
}
}


when {
process {
"""
input[0] = STAR_ALIGN.out.bam
input[1] = Channel.of([
[ id:'test_fasta' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
])
input[2] = Channel.of([
[ id:'test_gtf' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
])
input[3] = [[],[]]
input[4] = [[],[]]
input[5] = [[],[]]
input[6] = [[],[]]
input[7] = [[],[]]
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

}
161 changes: 161 additions & 0 deletions modules/nf-core/arriba/arriba/tests/main.nf.test.snap
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{
"homo_sapiens - single_end": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": true
},
"test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70"
]
],
"1": [
[
{
"id": "test",
"single_end": true
},
"test.fusions.discarded.tsv:md5,a35962c2fc4bc31321dde993363e71f1"
]
],
"2": [
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30"
],
"fusions": [
[
{
"id": "test",
"single_end": true
},
"test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70"
]
],
"fusions_fail": [
[
{
"id": "test",
"single_end": true
},
"test.fusions.discarded.tsv:md5,a35962c2fc4bc31321dde993363e71f1"
]
],
"versions": [
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-29T08:56:43.739605934"
},
"homo_sapiens - paired_end": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.discarded.tsv:md5,445cb87a27f063e751f93498cf8d10b5"
]
],
"2": [
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30"
],
"fusions": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.tsv:md5,7c3383f7eb6d79b84b0bd30a7ef02d70"
]
],
"fusions_fail": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.discarded.tsv:md5,445cb87a27f063e751f93498cf8d10b5"
]
],
"versions": [
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-29T08:59:40.552343349"
},
"homo_sapiens - paired_end - stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260"
]
],
"2": [
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30"
],
"fusions": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260"
]
],
"fusions_fail": [
[
{
"id": "test",
"single_end": false
},
"test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260"
]
],
"versions": [
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
},
"timestamp": "2024-04-29T08:33:36.830558897"
}
}
4 changes: 1 addition & 3 deletions ...les/nf-core/arriba/arriba/nextflow.config → ...-core/arriba/arriba/tests/nextflow.config
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@@ -1,9 +1,7 @@
process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: STAR_GENOMEGENERATE {
ext.args = '--genomeSAindexNbases 11'
ext.args = '--genomeSAindexNbases 9'
}

withName: STAR_ALIGN {
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/arriba/arriba/tests/tags.yml
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@@ -0,0 +1,2 @@
arriba/arriba:
- "modules/nf-core/arriba/arriba/**"
6 changes: 2 additions & 4 deletions modules/nf-core/star/align/environment.yml
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Expand Up @@ -4,7 +4,5 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::star=2.7.10a
- bioconda::samtools=1.18
- bioconda::htslib=1.18
- conda-forge::gawk=5.1.0
- bioconda::htslib=1.19.1
- bioconda::star=2.7.11b