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Update some module versions #6798

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Update some module versions #6798

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7cad6cd
Update modules for versions with ARM builds
pinin4fjords Oct 17, 2024
b250029
update picard containers
pinin4fjords Oct 17, 2024
2da8970
Fix containers for getchromsizes
pinin4fjords Oct 17, 2024
09fe447
Pick python version with ARM conda builds and biocontainer
pinin4fjords Oct 17, 2024
ca4e517
Fix other containers
pinin4fjords Oct 17, 2024
fd1811c
Remove quay.io
pinin4fjords Oct 18, 2024
7163ca0
Bump bedgraphtobigwig
pinin4fjords Oct 18, 2024
9bf7167
First batch of nf-test updates
pinin4fjords Oct 18, 2024
715b835
Second batch of nf-test updates
pinin4fjords Oct 18, 2024
4d79e8d
Update thests for liftovervcf
pinin4fjords Oct 18, 2024
39f24cf
One more nf-test update
pinin4fjords Oct 18, 2024
25e38cc
Last update: trimgalore
pinin4fjords Oct 18, 2024
1a95a3d
match conda cutadapt to trimgalore container
pinin4fjords Oct 18, 2024
1a66509
change r-base for picard
pinin4fjords Oct 18, 2024
f05b30b
[skip ci] nf-test migration for picard/collectrnaseqmetrics
pinin4fjords Oct 18, 2024
7f4825e
nf-test migration for picard/filtersamreads
pinin4fjords Oct 18, 2024
f87006e
Factor out setup
pinin4fjords Oct 18, 2024
015e9ee
Move bam checking to nft-bam
pinin4fjords Oct 18, 2024
4c0036b
Add missing tags
pinin4fjords Oct 18, 2024
03e5486
Merge branch 'master' into update_some_modules
pinin4fjords Oct 18, 2024
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4 changes: 2 additions & 2 deletions modules/nf-core/custom/getchromsizes/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@ channels:
- bioconda

dependencies:
- bioconda::htslib=1.20
- bioconda::samtools=1.20
- bioconda::htslib=1.21
- bioconda::samtools=1.21
4 changes: 2 additions & 2 deletions modules/nf-core/custom/getchromsizes/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
'biocontainers/samtools:1.20--h50ea8bc_0' }"
'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
'biocontainers/samtools:1.21--h50ea8bc_0' }"

input:
tuple val(meta), path(fasta)
Expand Down
40 changes: 20 additions & 20 deletions modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
]
],
"3": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
],
"fai": [
[
Expand All @@ -54,15 +54,15 @@
]
],
"versions": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-05T12:38:36.927106"
"timestamp": "2024-10-18T10:11:37.459094476"
},
"test_custom_getchromsizes": {
"content": [
Expand All @@ -87,7 +87,7 @@

],
"3": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
],
"fai": [
[
Expand All @@ -109,15 +109,15 @@
]
],
"versions": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-06-20T13:22:34.14237"
"timestamp": "2024-10-18T10:11:01.526301351"
},
"test_custom_getchromsizes_bgzip": {
"content": [
Expand Down Expand Up @@ -147,7 +147,7 @@
]
],
"3": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
],
"fai": [
[
Expand All @@ -174,15 +174,15 @@
]
],
"versions": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-06-20T13:23:06.241379"
"timestamp": "2024-10-18T10:11:14.32456385"
},
"test_custom_getchromsizes - stub": {
"content": [
Expand All @@ -207,7 +207,7 @@

],
"3": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
],
"fai": [
[
Expand All @@ -229,14 +229,14 @@
]
],
"versions": [
"versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f"
"versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-05T12:24:05.697845"
"timestamp": "2024-10-18T10:11:26.505487624"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/custom/tx2gene/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- python=3.9.5
- python=3.10.4
4 changes: 2 additions & 2 deletions modules/nf-core/custom/tx2gene/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process CUSTOM_TX2GENE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/python:3.9--1' :
'biocontainers/python:3.9--1' }"
'https://depot.galaxyproject.org/singularity/python:3.10.4' :
'biocontainers/python:3.10.4' }"

input:
tuple val(meta), path(gtf)
Expand Down
20 changes: 10 additions & 10 deletions modules/nf-core/custom/tx2gene/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,fb8145d7fbc6043ba031249b23ecda50"
"versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840"
],
"tx2gene": [
[
Expand All @@ -22,15 +22,15 @@
]
],
"versions": [
"versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50"
"versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-05T13:13:11.305047"
"timestamp": "2024-10-18T10:24:12.19104487"
},
"saccharomyces_cerevisiae - gtf - stub": {
"content": [
Expand All @@ -44,7 +44,7 @@
]
],
"1": [
"versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60"
"versions.yml:md5,48194bffef8cb833e82e31166f3d486c"
],
"tx2gene": [
[
Expand All @@ -55,14 +55,14 @@
]
],
"versions": [
"versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60"
"versions.yml:md5,48194bffef8cb833e82e31166f3d486c"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-10T15:15:34.064489"
"timestamp": "2024-10-18T10:24:24.729694098"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/picard/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::picard=3.2.0
- bioconda::picard=3.3.0
4 changes: 2 additions & 2 deletions modules/nf-core/picard/addorreplacereadgroups/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
'biocontainers/picard:3.2.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
'biocontainers/picard:3.3.0--hdfd78af_0' }"

input:
tuple val(meta), path(reads)
Expand Down
26 changes: 13 additions & 13 deletions modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
"content": [
"test.replaced.cram",
[
"versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
"versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-10T09:54:40.471730168"
"timestamp": "2024-10-18T10:13:23.115450366"
},
"sarscov2 - bam - stub": {
"content": [
Expand All @@ -30,7 +30,7 @@

],
"3": [
"versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
"versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
],
"bai": [

Expand All @@ -47,28 +47,28 @@

],
"versions": [
"versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
"versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-10T09:55:08.402649243"
"timestamp": "2024-10-18T10:13:47.23694937"
},
"sarscov2 - bam": {
"content": [
"null.replaced.bam",
"null.replaced.bai",
[
"versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
"versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-10T09:54:22.239968953"
"timestamp": "2024-10-18T10:12:53.083677142"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/picard/bedtointervallist/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::picard=3.2.0
- bioconda::picard=3.3.0
4 changes: 2 additions & 2 deletions modules/nf-core/picard/bedtointervallist/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process PICARD_BEDTOINTERVALLIST {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
'biocontainers/picard:3.2.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
'biocontainers/picard:3.3.0--hdfd78af_0' }"

input:
tuple val(meta) , path(bed)
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/picard/bedtointervallist/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:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
"versions.yml:md5,33540ea0c31ded2c1db95f82406034f8"
],
"interval_list": [
[
Expand All @@ -22,14 +22,14 @@
]
],
"versions": [
"versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65"
"versions.yml:md5,33540ea0c31ded2c1db95f82406034f8"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-26T10:39:08.82372"
"timestamp": "2024-10-18T10:17:35.308452582"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/picard/cleansam/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::picard=3.2.0
- bioconda::picard=3.3.0
4 changes: 2 additions & 2 deletions modules/nf-core/picard/cleansam/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process PICARD_CLEANSAM {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
'biocontainers/picard:3.2.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
'biocontainers/picard:3.3.0--hdfd78af_0' }"

input:
tuple val(meta), path(bam)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/picard/cleansam/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,13 @@
"content": [
"798439cbd7fd81cbcc5078022dc5479d",
[
"versions.yml:md5,f99b648dc3d150a0561094e3a142ee22"
"versions.yml:md5,412651954aecab12c868ee78cf9fa724"
]
],
"meta": {
"nf-test": "0.8.4",
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-26T10:36:05.525364"
"timestamp": "2024-10-18T10:46:32.969920917"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/picard/collecthsmetrics/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::picard=3.2.0
- bioconda::picard=3.3.0
4 changes: 2 additions & 2 deletions modules/nf-core/picard/collecthsmetrics/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process PICARD_COLLECTHSMETRICS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
'biocontainers/picard:3.2.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' :
'biocontainers/picard:3.3.0--hdfd78af_0' }"

input:
tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*')
Expand Down
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