Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bump openms version to 3.3.0 #7373

Open
wants to merge 14 commits into
base: master
Choose a base branch
from
Open

Bump openms version to 3.3.0 #7373

Show file tree
Hide file tree
Changes from 8 commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion modules/nf-core/openms/decoydatabase/environment.yml
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
10 changes: 5 additions & 5 deletions modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
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
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
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/idfilter/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process OPENMS_IDFILTER {

conda "bioconda::openms=3.2.0"
jonasscheid marked this conversation as resolved.
Show resolved Hide resolved
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 Down
20 changes: 10 additions & 10 deletions modules/nf-core/openms/idfilter/tests/main.nf.test.snap
View file
Open in desktop
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": "2025-01-27T09:53:09.504994933"
},
"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": "2025-01-27T09:53:02.555833293"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/idmassaccuracy/environment.yml
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
View file
Open in desktop
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
View file
Open in desktop
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
20 changes: 10 additions & 10 deletions modules/nf-core/openms/idripper/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
]
],
"1": [
"versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
"versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
],
"idxmls": [
[
Expand All @@ -28,15 +28,15 @@
]
],
"versions": [
"versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
"versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T12:02:51.318615048"
"timestamp": "2025-01-27T09:57:07.224001216"
},
"proteomics - split - idxml - stub": {
"content": [
Expand All @@ -53,7 +53,7 @@
]
],
"1": [
"versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
"versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
],
"idxmls": [
[
Expand All @@ -67,14 +67,14 @@
]
],
"versions": [
"versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948"
"versions.yml:md5,6bb62c7c19af0216ac52a3a446d8f902"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-10-08T12:02:59.481185212"
"timestamp": "2025-01-27T09:57:16.528990416"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/openms/idscoreswitcher/environment.yml
View file
Open in desktop
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/idscoreswitcher/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process OPENMS_IDSCORESWITCHER {

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(idxml)
Expand Down
Loading
Loading