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Update odgi to version 0.9.0 #7313

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merged 9 commits into from
Jan 23, 2025
Merged

Update odgi to version 0.9.0 #7313

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34816b7
Update odgi to version 0.9.0
heuermh Jan 15, 2025
9c34316
Update nf-test checksums
heuermh Jan 15, 2025
22652d5
Merge branch 'master' into odgi-0.9.0
heuermh Jan 15, 2025
d722598
Assert output file(s) exist
heuermh Jan 17, 2025
10dafcb
Merge branch 'master' into odgi-0.9.0
heuermh Jan 17, 2025
f9fc2c0
Merge branch 'master' into odgi-0.9.0
subwaystation Jan 20, 2025
abd01ab
Merge branch 'master' into odgi-0.9.0
heuermh Jan 22, 2025
58c7b35
Assert versions match
heuermh Jan 22, 2025
71f1f8a
Update test snapshots
heuermh Jan 22, 2025
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2 changes: 1 addition & 1 deletion modules/nf-core/odgi/build/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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/build/main.nf
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Expand Up @@ -4,8 +4,8 @@ process ODGI_BUILD {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graph)
Expand Down
5 changes: 2 additions & 3 deletions modules/nf-core/odgi/build/tests/main.nf.test
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Expand Up @@ -25,10 +25,9 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
// { assert snapshot(process.out).match() } // the odgi file on disk may not be deterministic, but the graph itself is
{ assert snapshot(process.out.versions).match()},
{ assert path(process.out.og.get(0).get(1)).exists() } // the odgi file on disk may not be deterministic, but the graph itself is
)
}

}

}
35 changes: 8 additions & 27 deletions modules/nf-core/odgi/build/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,33 +1,14 @@
{
"homo_sapiens - pangenome - pangenome_smoothxg_gfa": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.og:md5,8660c0f724a54d7346575ac38ff0b329"
]
],
"1": [
"versions.yml:md5,57e730c18f2ab7d51bd8ca113e39d553"
],
"og": [
[
{
"id": "test",
"single_end": false
},
"test.og:md5,8660c0f724a54d7346575ac38ff0b329"
]
],
"versions": [
"versions.yml:md5,57e730c18f2ab7d51bd8ca113e39d553"
]
}
[
"versions.yml:md5,ac55cdc779839b4b8de83f0a757c8671"
]
],
"timestamp": "2024-01-30T11:07:44.462811986"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-22T10:31:31.313418"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/odgi/draw/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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/draw/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process ODGI_DRAW {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graph), path(lay)
Expand Down
2 changes: 0 additions & 2 deletions modules/nf-core/odgi/draw/tests/main.nf.test
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Expand Up @@ -29,7 +29,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
14 changes: 9 additions & 5 deletions modules/nf-core/odgi/draw/tests/main.nf.test.snap
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Expand Up @@ -8,26 +8,30 @@
"id": "test",
"single_end": false
},
"test.png:md5,2024bc28ff028163094fa1070da028db"
"test.png:md5,be625ee96d1acd50ba6dbb37102ae6b9"
]
],
"1": [
"versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3"
"versions.yml:md5,227b8d9ac064dec15f0abad54334e4fa"
],
"png": [
[
{
"id": "test",
"single_end": false
},
"test.png:md5,2024bc28ff028163094fa1070da028db"
"test.png:md5,be625ee96d1acd50ba6dbb37102ae6b9"
]
],
"versions": [
"versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3"
"versions.yml:md5,227b8d9ac064dec15f0abad54334e4fa"
]
}
],
"timestamp": "2024-01-30T11:03:39.412763234"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-15T14:46:28.331207"
}
}
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missing EOL

2 changes: 1 addition & 1 deletion modules/nf-core/odgi/layout/environment.yml
View file
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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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/layout/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process ODGI_LAYOUT {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graph)
Expand Down
7 changes: 4 additions & 3 deletions modules/nf-core/odgi/layout/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -26,10 +26,11 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
// { assert snapshot(process.out).match() } // odgi layout is not deterministic
{ assert snapshot(process.out.versions).match()},
// odgi layout is not deterministic
{ assert path(process.out.lay.get(0).get(1)).exists() },
{ assert path(process.out.tsv.get(0).get(1)).exists() }
)
}

}

}
53 changes: 8 additions & 45 deletions modules/nf-core/odgi/layout/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,51 +1,14 @@
{
"homo_sapiens - pangenome - pangenome_smoothxg_gfa": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.lay:md5,ce4ee2f434717077f5c765a5a82fd978"
]
],
"1": [
[
{
"id": "test",
"single_end": false
},
"test.tsv:md5,7bf353889ac6dfcce8b38618d760f144"
]
],
"2": [
"versions.yml:md5,c0207add403de5e7011f368a4cfd3b2b"
],
"lay": [
[
{
"id": "test",
"single_end": false
},
"test.lay:md5,ce4ee2f434717077f5c765a5a82fd978"
]
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test.tsv:md5,7bf353889ac6dfcce8b38618d760f144"
]
],
"versions": [
"versions.yml:md5,c0207add403de5e7011f368a4cfd3b2b"
]
}
[
"versions.yml:md5,ee823dcfb065a7234f0c4e2241651939"
]
],
"timestamp": "2024-01-30T10:58:20.958731752"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2025-01-22T10:31:46.13426"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/odgi/sort/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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/sort/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process ODGI_SORT {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graph)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/odgi/sort/tests/main.nf.test.snap
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Expand Up @@ -3,13 +3,13 @@
"content": [
"test.og",
[
"versions.yml:md5,6defcba99b79fde2042de15eec929bf4"
"versions.yml:md5,642e4ce5c2288d3b6e4f231396ecd5b4"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-08-13T09:40:56.821872"
"timestamp": "2025-01-15T14:47:49.015053"
}
}
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missing EOL

2 changes: 1 addition & 1 deletion modules/nf-core/odgi/squeeze/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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/squeeze/main.nf
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Expand Up @@ -4,8 +4,8 @@ process ODGI_SQUEEZE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graphs)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/odgi/squeeze/tests/main.nf.test.snap
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Expand Up @@ -3,13 +3,13 @@
"content": [
"test.og",
[
"versions.yml:md5,ee7ed77636f98e98a3e40a915c22ed64"
"versions.yml:md5,751fb4a0629a070f0edc989c4d5e555b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-08-13T10:09:07.409463"
"timestamp": "2025-01-15T14:48:22.366465"
}
}
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missing EOL

2 changes: 1 addition & 1 deletion modules/nf-core/odgi/stats/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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/stats/main.nf
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Expand Up @@ -4,8 +4,8 @@ process ODGI_STATS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graph)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/odgi/stats/tests/main.nf.test.snap
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Expand Up @@ -3,13 +3,13 @@
"content": [
"test.og.stats.tsv",
[
"versions.yml:md5,0f4d685d1c0d3562081073bfbf85d95d"
"versions.yml:md5,5127b79951be7dcc7925348293826aea"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-08-09T09:55:15.438306"
"timestamp": "2025-01-15T14:48:52.45995"
}
}
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missing EOL

2 changes: 1 addition & 1 deletion modules/nf-core/odgi/unchop/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::odgi=0.8.4
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missing EOL

- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/unchop/main.nf
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Expand Up @@ -4,8 +4,8 @@ process ODGI_UNCHOP {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

input:
tuple val(meta), path(graph)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/odgi/unchop/tests/main.nf.test.snap
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Expand Up @@ -3,13 +3,13 @@
"content": [
"test.og",
[
"versions.yml:md5,721a9406e96a94ccb0ec44dc4f76ed09"
"versions.yml:md5,23b7ff2375170fe1ed6a50e018fbefb1"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.3"
},
"timestamp": "2024-08-13T09:38:53.743369"
"timestamp": "2025-01-15T14:49:21.848525"
}
}
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missing EOL

2 changes: 1 addition & 1 deletion modules/nf-core/odgi/view/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::odgi=0.8.4
- bioconda::odgi=0.9.0
4 changes: 2 additions & 2 deletions modules/nf-core/odgi/view/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process ODGI_VIEW {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0':
'biocontainers/odgi:0.8.4--py310h6cc9453_0' }"
'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1':
'biocontainers/odgi:0.9.0--py312h5e9d817_1' }"

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