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Bump openms version to 3.3.0 #7373

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Bump openms version to 3.3.0 #7373

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2a52770
update container version-tag
jonasscheid Oct 8, 2024
1bc6755
update snapshots
jonasscheid Oct 8, 2024
3821e7d
Merge branch 'nf-core:master' into master
jonasscheid Jan 13, 2025
49bd20e
Merge branch 'nf-core:master' into master
jonasscheid Jan 22, 2025
db90f42
Merge branch 'nf-core:master' into master
jonasscheid Jan 27, 2025
76726e7
bump openms version
jonasscheid Jan 27, 2025
ab4d5c3
batch update nf-test snapshots
jonasscheid Jan 27, 2025
1b288fc
Merge branch 'master' into master
famosab Jan 27, 2025
bd8d9bb
update snapshots, conda version for idfilter, first attempt restructu…
jonasscheid Jan 30, 2025
1ee643e
Merge branch 'master' of https://github.com/jonasscheid/modules
jonasscheid Jan 30, 2025
53a3180
Merge branch 'master' into master
jonasscheid Jan 30, 2025
1fe7669
fix lint
jonasscheid Jan 30, 2025
7671daf
Merge branch 'master' of https://github.com/jonasscheid/modules
jonasscheid Jan 30, 2025
d2d620e
fix lint again
jonasscheid Jan 30, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/openms/decoydatabase/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::openms=3.2.0
- bioconda::openms=3.3.0
4 changes: 2 additions & 2 deletions modules/nf-core/openms/decoydatabase/main.nf
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Expand Up @@ -4,8 +4,8 @@ process OPENMS_DECOYDATABASE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
'biocontainers/openms:3.2.0--haddbca4_4' }"
'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(fasta)
Expand Down
3 changes: 0 additions & 3 deletions modules/nf-core/openms/decoydatabase/tests/main.nf.test
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Expand Up @@ -18,7 +18,6 @@ nextflow_process {
[id:'test'],
file(params.modules_testdata_base_path + 'proteomics/database/yeast_UPS.fasta', checkIfExists: true)
]

"""
}
}
Expand All @@ -29,7 +28,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
10 changes: 5 additions & 5 deletions modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap
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Expand Up @@ -11,7 +11,7 @@
]
],
"1": [
"versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426"
"versions.yml:md5,da0a498551f58bedc67c2ff26cc99f54"
],
"decoy_fasta": [
[
Expand All @@ -22,14 +22,14 @@
]
],
"versions": [
"versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426"
"versions.yml:md5,da0a498551f58bedc67c2ff26cc99f54"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T11:22:32.701406062"
"timestamp": "2025-01-27T09:32:00.741200995"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/filefilter/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::openms=3.2.0"
- "bioconda::openms=3.3.0"
4 changes: 2 additions & 2 deletions modules/nf-core/openms/filefilter/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process OPENMS_FILEFILTER {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
'biocontainers/openms:3.2.0--haddbca4_4' }"
'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(file)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/openms/filefilter/tests/main.nf.test.snap
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Expand Up @@ -43,7 +43,7 @@

],
"3": [
"versions.yml:md5,a8ec8f78f4a0da0328482bf90dc2df00"
"versions.yml:md5,2dbaab2d39324e978b6b63643b2adee6"
],
"consensusxml": [

Expand All @@ -60,14 +60,14 @@
]
],
"versions": [
"versions.yml:md5,a8ec8f78f4a0da0328482bf90dc2df00"
"versions.yml:md5,2dbaab2d39324e978b6b63643b2adee6"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nextflow": "24.10.4"
},
"timestamp": "2025-01-21T13:09:28.723787747"
"timestamp": "2025-01-27T09:52:55.262478412"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/idfilter/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::openms=3.2.0"
- "bioconda::openms=3.3.0"
8 changes: 5 additions & 3 deletions modules/nf-core/openms/idfilter/main.nf
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Expand Up @@ -2,10 +2,10 @@ process OPENMS_IDFILTER {
tag "$meta.id"
label 'process_single'

conda "bioconda::openms=3.2.0"
conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
'biocontainers/openms:3.2.0--haddbca4_4' }"
'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(id_file), path(filter_file)
Expand All @@ -21,6 +21,7 @@ process OPENMS_IDFILTER {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "${id_file.getExtension()}"
if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
// Optional filtering via filter_file
def filter_citerion = task.ext.args2 ?: "-whitelist:peptides"
def filter = filter_file ? "${filter_citerion} ${filter_file}" : ""
Expand All @@ -42,6 +43,7 @@ process OPENMS_IDFILTER {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "${id_file.getExtension()}"
if ("$file" == "${prefix}.${suffix}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
// Optional filtering via filter_file
def filter_citerion = task.ext.args2 ?: "-whitelist:peptides"
def filter = filter_file ? "${filter_citerion} ${filter_file}" : ""
Expand Down
20 changes: 10 additions & 10 deletions modules/nf-core/openms/idfilter/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
]
],
"1": [
"versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
"versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
],
"filtered": [
[
Expand All @@ -22,15 +22,15 @@
]
],
"versions": [
"versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
"versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T11:45:00.758602574"
"timestamp": "2025-01-27T14:24:13.027097196"
},
"proteomics - filter - idxml": {
"content": [
Expand All @@ -44,7 +44,7 @@
]
],
"1": [
"versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
"versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
],
"filtered": [
[
Expand All @@ -55,14 +55,14 @@
]
],
"versions": [
"versions.yml:md5,8a95c69294e90ae931b766218dc87dec"
"versions.yml:md5,d1e4fc495db4455433af0f1c9944fa4a"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T11:44:53.291545021"
"timestamp": "2025-01-27T14:24:01.067382973"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/idmassaccuracy/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::openms=3.2.0"
- "bioconda::openms=3.3.0"
4 changes: 2 additions & 2 deletions modules/nf-core/openms/idmassaccuracy/main.nf
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Expand Up @@ -4,8 +4,8 @@ process OPENMS_IDMASSACCURACY {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
'biocontainers/openms:3.2.0--haddbca4_4' }"
'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(mzmls), path(idxmls)
Expand Down
20 changes: 10 additions & 10 deletions modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap
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Expand Up @@ -19,7 +19,7 @@
]
],
"2": [
"versions.yml:md5,9bf83a6db02732d209de6819818aed26"
"versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
],
"frag_err": [
[
Expand All @@ -38,15 +38,15 @@
]
],
"versions": [
"versions.yml:md5,9bf83a6db02732d209de6819818aed26"
"versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T11:26:08.231171982"
"timestamp": "2025-01-27T09:38:35.753866654"
},
"proteomics - openms - mass_error": {
"content": [
Expand All @@ -63,7 +63,7 @@

],
"2": [
"versions.yml:md5,9bf83a6db02732d209de6819818aed26"
"versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
],
"frag_err": [
[
Expand All @@ -77,14 +77,14 @@

],
"versions": [
"versions.yml:md5,9bf83a6db02732d209de6819818aed26"
"versions.yml:md5,3ef5990b5bbae77d5faba3fead83814c"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T11:25:57.38948188"
"timestamp": "2025-01-27T09:38:24.74497273"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/idmerger/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::openms=3.2.0
- bioconda::openms=3.3.0
4 changes: 2 additions & 2 deletions modules/nf-core/openms/idmerger/main.nf
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Expand Up @@ -4,8 +4,8 @@ process OPENMS_IDMERGER {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' :
'biocontainers/openms:3.2.0--haddbca4_4' }"
'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8' :
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(idxmls)
Expand Down
18 changes: 9 additions & 9 deletions modules/nf-core/openms/idmerger/tests/main.nf.test.snap
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Expand Up @@ -2,14 +2,14 @@
"proteomics - openms - idxml": {
"content": [
[
"versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
"versions.yml:md5,223c9352a3e79162fde8cbbf18e93e54"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T12:02:35.595648853"
"timestamp": "2025-01-27T09:56:47.184737888"
},
"proteomics - openms - idxml - stub": {
"content": [
Expand All @@ -23,7 +23,7 @@
]
],
"1": [
"versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
"versions.yml:md5,223c9352a3e79162fde8cbbf18e93e54"
],
"idxml": [
[
Expand All @@ -34,14 +34,14 @@
]
],
"versions": [
"versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3"
"versions.yml:md5,223c9352a3e79162fde8cbbf18e93e54"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T12:02:42.76246364"
"timestamp": "2025-01-27T09:56:54.134223267"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/idripper/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::openms=3.2.0"
- "bioconda::openms=3.3.0"
4 changes: 2 additions & 2 deletions modules/nf-core/openms/idripper/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process OPENMS_IDRIPPER {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4':
'biocontainers/openms:3.2.0--haddbca4_4' }"
'https://depot.galaxyproject.org/singularity/openms:3.3.0--h0656172_8':
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(merged_idxml)
Expand Down
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