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Merged
merged 46 commits into from
Oct 7, 2025
Merged

Gzi input for mutect2 #9043

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6710870
Updated Mutect2 input for gwi in main.nf and meta.yml with more gz me…
apetizerr Sep 8, 2025
7dc4450
updated existing test with gzi input
apetizerr Sep 10, 2025
9ee9cc7
Merge branch 'nf-core:master' into master
apetizerr Sep 10, 2025
f444782
Adding path to gzi
apetizerr Sep 11, 2025
2fa41ed
added gz and gzi options onto the yml
apetizerr Sep 11, 2025
7fcf067
added gzi blank input options
apetizerr Sep 11, 2025
e35b4ae
added test for gzi input for modified mitochondria test
apetizerr Sep 11, 2025
ba68b7a
Merge branch 'master' of https://github.com/apetizerr/modules
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11a4161
Merge branch 'master' of https://github.com/apetizerr/modules
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04568c1
updating snapshot for mitochondria gz test
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70f10c5
Merge branch 'nf-core:master' into master
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918f748
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25f7606
Delete .idea/.gitignore
apetizerr Sep 12, 2025
cfa3179
new input for gzi in meta path
apetizerr Sep 15, 2025
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Merge branch 'nf-core:master' into master
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dd047c5
new input for gzi, included in yml and test case
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famosab Sep 18, 2025
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Update modules/nf-core/gatk4/mutect2/meta.yml
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Update modules/nf-core/gatk4/mutect2/meta.yml
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42d7d42
Update modules/nf-core/gatk4/mutect2/main.nf
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Update modules/nf-core/gatk4/mutect2/tests/main.nf.test
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Update modules/nf-core/gatk4/mutect2/main.nf
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Merge branch 'nf-core:master' into master
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652b05d
test changes for gzi and fai input
apetizerr Sep 19, 2025
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Merge branch 'master' into master
famosab Sep 19, 2025
7fe355c
Update modules/nf-core/gatk4/mutect2/meta.yml
famosab Sep 19, 2025
d9fc032
gzi input options
apetizerr Sep 22, 2025
eeabf8a
adding the input for gzi
apetizerr Sep 22, 2025
bd7cbfe
fixing gzi input on val meta
apetizerr Sep 22, 2025
f034d34
empty gzi input
apetizerr Sep 25, 2025
46ecc88
test update for empty gzi input
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apetizerr Oct 3, 2025
79f614b
Update GATK4 Mutect2 test snapshots
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Merge branch 'nf-core:master' into master
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2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/mutect2/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ process GATK4_MUTECT2 {
input:
tuple val(meta), path(input), path(input_index), path(intervals)
tuple val(meta2), path(fasta)
tuple val(meta3), path(fai)
tuple val(meta3), path(fai), path(gzi)
tuple val(meta4), path(dict)
path alleles
path alleles_tbi
Expand Down
11 changes: 8 additions & 3 deletions modules/nf-core/gatk4/mutect2/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ input:
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
pattern: "*.{fasta,fasta.gz}"
ontologies: []
- - meta3:
type: map
Expand All @@ -56,7 +56,12 @@ input:
- fai:
type: file
description: Index of reference fasta file
pattern: "*.fasta.fai"
pattern: "*.{fasta.fai,fasta.fai.gz}"
ontologies: []
- gzi:
type: file
description: Index of bgzipped reference fasta file
pattern: "*.fasta.gz.gzi"
ontologies: []
- - meta4:
type: map
Expand Down Expand Up @@ -154,4 +159,4 @@ authors:
maintainers:
- "@GCJMackenzie"
- "@ramprasadn"


78 changes: 69 additions & 9 deletions modules/nf-core/gatk4/mutect2/tests/main.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -101,7 +102,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -151,7 +153,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -201,7 +204,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -251,7 +255,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -301,7 +306,59 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
]
input[4] = []
input[5] = []
input[6] = []
input[7] = []
input[8] = []
input[9] = []
"""
}
}
then {
assertAll(
{ assert process.success },
{
assert snapshot(
path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
process.out.tbi.collect { file(it[1]).getName() },
process.out.stats,
process.out.f1r2,
process.out.versions
).match()
}
)
}
}

test("mitochondria - bam - gz_ref"){
when {
params {
module_args = "--mitochondria-mode"
}
process {
"""
input[0] = [
[ id:'test'],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam', checkIfExists: true)],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai', checkIfExists: true)],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)]
]
input[1] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true)
]
input[2] = [
[ id:'genome' ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true)],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true)]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -364,7 +421,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -417,7 +475,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down Expand Up @@ -468,7 +527,8 @@ nextflow_process {
]
input[2] = [
[ id:'genome' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)],
[]
]
input[3] = [
[ id:'genome' ],
Expand Down
45 changes: 36 additions & 9 deletions modules/nf-core/gatk4/mutect2/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"human - bam - generate_pon": {
"content": [
"876aa6be01c0c8fc71ad8e99ed842240",
"c3b555d00c575478b65626f56e3085c4",
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any idea why all of these md5sums change even though we changed nothing about thr module itself? 🤔

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i ran the tests for other modules since i was moving the inputs around

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but still the bam readsMD5 sum should not change just because you add an empty input

[
"test.vcf.gz.tbi"
],
Expand All @@ -24,11 +24,11 @@
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-15T16:10:57.549285793"
"timestamp": "2025-09-14T17:03:47.925701"
},
"human - bam - tumor_only - force_call": {
"content": [
"9c2928d0e751262c048ac162b9223e4e",
"93b22af80151fa3828e79bd522f9379",
[
"test.vcf.gz.tbi"
],
Expand All @@ -51,7 +51,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-15T16:21:08.898433486"
"timestamp": "2025-09-15T10:16:14.477947"
},
"human - bam - tumor_normal_pair": {
"content": [
Expand Down Expand Up @@ -84,7 +84,7 @@
},
"human - cram": {
"content": [
"1b65f1a163b517944bf2e4b74230e035",
"6a839307b251fbeb1a4b08e3b3692513",
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I think these changes should not have happened - I guess that they are due to the platform you ran the tests on. I had these issues sometimes when running directly on my mac. We have multiple possibilities to solve this: either switch to a linux workstation or run it in gitpod :)

[
"test.vcf.gz.tbi"
],
Expand Down Expand Up @@ -138,7 +138,7 @@
},
"human - bam - tumor_only": {
"content": [
"1b65f1a163b517944bf2e4b74230e035",
"6a839307b251fbeb1a4b08e3b3692513",
[
"test.vcf.gz.tbi"
],
Expand All @@ -161,11 +161,38 @@
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-15T16:03:45.457449363"
"timestamp": "2025-09-14T16:46:30.35196"
},
"mitochondria - bam - gz_ref": {
"content": [
"ea70f79e33805a2c0b47b32a48a8d26f",
[
"test.vcf.gz.tbi"
],
[
[
{
"id": "test"
},
"test.vcf.gz.stats:md5,fc6ea14ca2da346babe78161beea28c9"
]
],
[

],
[
"versions.yml:md5,bbf6869d6ef6dbd05a2a538d70e0fd3d"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-18T21:58:13.575194"
},
"human - bam - tumor_normal_pair - force_call": {
"content": [
"63c4ff01a8316f4243b6b12b06ded74e",
"8f343e641476d582afd1efca801e30fe",
[
"test.vcf.gz.tbi"
],
Expand All @@ -190,7 +217,7 @@
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2025-09-15T16:17:00.767220472"
"timestamp": "2025-09-14T23:49:18.290784"
},
"human - bam - tumor_normal_pair_f1r2 - stub": {
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Now the results for this test are completely empty....

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I requested to join the github org and invited to give access

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Since there is a limit to the number of times i can use ONA to test, should I set up my environment in windows OS and not mac to avoid the checksum troubles?

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No I think either we use linux or I will try and run it on my linux workstation locally

"content": [
Expand Down
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