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bump ALL gatk4 modules #6917

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bump ALL gatk4 modules #6917

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4d73bd8
bump gatk4
matthdsm Oct 31, 2024
c581acf
fix some tests
matthdsm Oct 31, 2024
4cc9150
more tests
matthdsm Oct 31, 2024
9ddb1a2
more tests
matthdsm Oct 31, 2024
552f40e
Merge branch 'master' into bump/gatk
matthdsm Oct 31, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/addorreplacereadgroups/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::gatk4=4.5.0.0
- bioconda::gatk4=4.6.1.0
4 changes: 2 additions & 2 deletions modules/nf-core/gatk4/addorreplacereadgroups/main.nf
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Expand Up @@ -4,8 +4,8 @@ process GATK4_ADDORREPLACEREADGROUPS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0':
'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }"

input:
tuple val(meta), path(bam)
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18 changes: 9 additions & 9 deletions modules/nf-core/gatk4/addorreplacereadgroups/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@

],
"3": [
"versions.yml:md5,da55295b55986cfcf65d41745c7bda4c"
"versions.yml:md5,09f498302943b70029a56ddf65522814"
],
"bai": [
[
Expand All @@ -54,27 +54,27 @@

],
"versions": [
"versions.yml:md5,da55295b55986cfcf65d41745c7bda4c"
"versions.yml:md5,09f498302943b70029a56ddf65522814"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-03-20T13:19:33.815262"
"timestamp": "2024-10-31T10:28:22.832793576"
},
"versions": {
"content": [
[
"versions.yml:md5,da55295b55986cfcf65d41745c7bda4c"
"versions.yml:md5,09f498302943b70029a56ddf65522814"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-03-20T13:19:18.103325"
"timestamp": "2024-10-31T10:28:10.146204216"
},
"cram_name": {
"content": [
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/annotateintervals/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::gatk4=4.5.0.0
- bioconda::gatk4=4.6.1.0
4 changes: 2 additions & 2 deletions modules/nf-core/gatk4/annotateintervals/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process GATK4_ANNOTATEINTERVALS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0':
'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }"

input:
tuple val(meta), path(intervals)
Expand Down
58 changes: 29 additions & 29 deletions modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
]
],
"1": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
],
"annotated_intervals": [
[
Expand All @@ -24,15 +24,15 @@
]
],
"versions": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.0"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-02-13T16:07:36.32193"
"timestamp": "2024-10-31T10:29:29.006068994"
},
"homo_sapiens genome [interval_list]": {
"content": [
Expand All @@ -47,7 +47,7 @@
]
],
"1": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
],
"annotated_intervals": [
[
Expand All @@ -59,15 +59,15 @@
]
],
"versions": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.0"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-02-13T16:08:12.533176"
"timestamp": "2024-10-31T10:30:08.763305448"
},
"homo_sapiens genome multi-interval [bed]": {
"content": [
Expand All @@ -82,7 +82,7 @@
]
],
"1": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
],
"annotated_intervals": [
[
Expand All @@ -94,15 +94,15 @@
]
],
"versions": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.0"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-02-13T16:07:54.643276"
"timestamp": "2024-10-31T10:29:48.403638052"
},
"homo_sapiens genome [interval_list] mappable_regions": {
"content": [
Expand All @@ -117,7 +117,7 @@
]
],
"1": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
],
"annotated_intervals": [
[
Expand All @@ -129,28 +129,28 @@
]
],
"versions": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.0"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-02-13T16:08:31.311782"
"timestamp": "2024-10-31T10:30:23.256626974"
},
"homo_sapiens genome [bed] - stub": {
"content": [
[
"test.tsv",
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.0"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-02-13T16:09:04.54745"
"timestamp": "2024-10-31T10:30:52.179735439"
},
"homo_sapiens genome [interval_list] duplication_regions": {
"content": [
Expand All @@ -165,7 +165,7 @@
]
],
"1": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
],
"annotated_intervals": [
[
Expand All @@ -177,14 +177,14 @@
]
],
"versions": [
"versions.yml:md5,599cde136feb5d60b2d01b5fbd252fa0"
"versions.yml:md5,6e1e1caad2a19737e858bc743284cbb2"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.0"
"nf-test": "0.9.1",
"nextflow": "24.10.0"
},
"timestamp": "2024-02-13T16:08:49.684766"
"timestamp": "2024-10-31T10:30:37.398809104"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/applybqsr/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::gatk4=4.5.0.0
- bioconda::gatk4=4.6.1.0
4 changes: 2 additions & 2 deletions modules/nf-core/gatk4/applybqsr/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0':
'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.6.1.0--py310hdfd78af_0':
'biocontainers/gatk4:4.6.1.0--py310hdfd78af_0' }"

input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
Expand Down
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