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Update version modules tcoffee to 13.46.1 #7498

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Update version modules tcoffee to 13.46.1 #7498

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Update modules tcoffee
luisas Feb 19, 2025
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3 changes: 1 addition & 2 deletions modules/nf-core/tcoffee/align/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::t-coffee=13.46.0.919e8c6b
- bioconda::tmalign=20170708
- bioconda::t-coffee=13.46.1.b8b01e06
- conda-forge::pigz=2.8
4 changes: 2 additions & 2 deletions modules/nf-core/tcoffee/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TCOFFEE_ALIGN {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'oras://community.wave.seqera.io/library/t-coffee_tmalign_pigz:f861f2f8f266c2fe':
'community.wave.seqera.io/library/t-coffee_tmalign_pigz:be7dac2ae6aba380' }"
'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"

input:
tuple val(meta) , path(fasta)
Expand Down
46 changes: 23 additions & 23 deletions modules/nf-core/tcoffee/align/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,62 +2,62 @@
"align_sequence - uncompressed - seatoxin": {
"content": [
[
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-09-16T10:38:34.006567221"
"timestamp": "2025-02-19T08:01:20.749130634"
},
"align_with_structure - uncompressed - seatoxin": {
"content": [
[
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nextflow": "24.10.4"
},
"timestamp": "2024-12-17T19:36:55.402470994"
"timestamp": "2025-02-19T08:01:53.240805233"
},
"align_sequence - compressed - seatoxin": {
"content": [
[
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-09-16T10:38:18.99603304"
"timestamp": "2025-02-19T08:01:05.500957902"
},
"align_with_guide_tree - uncompressed - seatoxin": {
"content": [
[
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-09-16T10:38:48.044669392"
"timestamp": "2025-02-19T08:01:36.781063137"
},
"align_with_lib - seatoxin": {
"content": [
[
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-09-16T10:47:34.909457138"
"timestamp": "2025-02-19T08:02:04.884176473"
},
"align_sequence - uncompressed - seatoxin - stub": {
"content": [
Expand All @@ -74,7 +74,7 @@

],
"2": [
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
],
"alignment": [
[
Expand All @@ -88,14 +88,14 @@

],
"versions": [
"versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
"versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.3"
"nextflow": "24.10.4"
},
"timestamp": "2024-12-17T19:37:06.112822121"
"timestamp": "2025-02-19T08:02:17.843814218"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/tcoffee/alncompare/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::t-coffee=13.46.0.919e8c6b
- bioconda::t-coffee=13.46.1.b8b01e06
- conda-forge::pigz=2.8
8 changes: 6 additions & 2 deletions modules/nf-core/tcoffee/alncompare/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TCOFFEE_ALNCOMPARE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"

input:
tuple val(meta), path(msa), path(ref_msa)
Expand Down Expand Up @@ -33,6 +33,8 @@ process TCOFFEE_ALNCOMPARE {
fi

export TEMP='./'
export TMP_4_TCOFFEE="./"
export HOME="./"
t_coffee -other_pg aln_compare \
-al1 ${ref_msa} \
-al2 uncompressed_msa.fa \
Expand Down Expand Up @@ -60,6 +62,8 @@ process TCOFFEE_ALNCOMPARE {
"""
# Otherwise, tcoffee will crash when calling its version
export TEMP='./'
export TMP_4_TCOFFEE="./"
export HOME="./"
touch "${prefix}.scores"

cat <<-END_VERSIONS > versions.yml
Expand Down
28 changes: 14 additions & 14 deletions modules/nf-core/tcoffee/alncompare/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:md5,438507517a1a831c7b7a1571b1fdd98d"
"versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
],
"scores": [
[
Expand All @@ -22,15 +22,15 @@
]
],
"versions": [
"versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
"versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.1"
"nextflow": "24.10.4"
},
"timestamp": "2024-11-26T08:54:31.823528877"
"timestamp": "2025-02-19T08:10:13.98747038"
},
"seatoxin - stub": {
"content": [
Expand All @@ -44,7 +44,7 @@
]
],
"1": [
"versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
"versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
],
"scores": [
[
Expand All @@ -55,15 +55,15 @@
]
],
"versions": [
"versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
"versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-09-16T09:48:00.328461809"
"timestamp": "2025-02-19T08:10:31.783898713"
},
"seatoxin": {
"content": [
Expand All @@ -77,7 +77,7 @@
]
],
"1": [
"versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
"versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
],
"scores": [
[
Expand All @@ -88,14 +88,14 @@
]
],
"versions": [
"versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
"versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2024-01-22T17:08:59.494237269"
"timestamp": "2025-02-19T08:10:01.028826144"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/tcoffee/consensus/environment.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::t-coffee=13.46.0.919e8c6b
- bioconda::t-coffee=13.46.1.b8b01e06
- conda-forge::pigz=2.8
10 changes: 7 additions & 3 deletions modules/nf-core/tcoffee/consensus/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,8 @@ process TCOFFEE_CONSENSUS {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5e/5e5c1c07cc0099dacea172348bc78f9a9baab592ce3ece89873703b9e963d269/data':
'community.wave.seqera.io/library/t-coffee_pigz:c98a6c87c62d9df6' }"

'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"

input:
tuple val(meta) , path(aln)
Expand All @@ -29,6 +28,9 @@ process TCOFFEE_CONSENSUS {
def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.aln.gz" : ""
"""
export TEMP='./'
export TMP_4_TCOFFEE="./"
export HOME="./"

t_coffee -aln ${aln} \
$tree_args \
$args \
Expand All @@ -47,6 +49,8 @@ process TCOFFEE_CONSENSUS {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
export TEMP='./'
export TMP_4_TCOFFEE="./"
export HOME="./"
touch ${prefix}.aln${compress ? '.gz':''}

cat <<-END_VERSIONS > versions.yml
Expand Down
44 changes: 30 additions & 14 deletions modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,15 @@
"consensus - no tree - uncompressed - seatoxin ": {
"content": [
[
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
"versions.yml:md5,96aeed9939a911a37421af7e88431a26",
"versions.yml:md5,96aeed9939a911a37421af7e88431a26"
]
],
"timestamp": "2024-09-18T13:54:43.924522245"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-19T09:13:46.582982023"
},
"consensus - stub": {
"content": [
Expand All @@ -29,8 +33,8 @@

],
"2": [
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
"versions.yml:md5,96aeed9939a911a37421af7e88431a26",
"versions.yml:md5,96aeed9939a911a37421af7e88431a26"
],
"alignment": [
[
Expand All @@ -50,29 +54,41 @@

],
"versions": [
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
"versions.yml:md5,96aeed9939a911a37421af7e88431a26",
"versions.yml:md5,96aeed9939a911a37421af7e88431a26"
]
}
],
"timestamp": "2024-10-18T11:41:11.216683"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-19T09:14:44.325890293"
},
"consensus - tree - compressed- seatoxin": {
"content": [
[
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
"versions.yml:md5,96aeed9939a911a37421af7e88431a26",
"versions.yml:md5,96aeed9939a911a37421af7e88431a26"
]
],
"timestamp": "2024-09-18T13:55:03.627733582"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-19T09:14:24.230709196"
},
"consensus_evaluation - no tree - uncompressed - seatoxin ": {
"content": [
[
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
"versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
"versions.yml:md5,96aeed9939a911a37421af7e88431a26",
"versions.yml:md5,96aeed9939a911a37421af7e88431a26"
]
],
"timestamp": "2024-10-18T11:43:51.839734"
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.4"
},
"timestamp": "2025-02-19T09:14:05.703271958"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/tcoffee/extractfrompdb/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::t-coffee=13.46.0.919e8c6b
- bioconda::t-coffee=13.46.1.b8b01e06
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