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fix calder version #10810

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fix calder version #10810

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07c270d
fix calder version
carolineclbcq-fr Mar 13, 2026
b05129b
Merge branch 'master' into calder2_topic
SPPearce Mar 16, 2026
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15 changes: 2 additions & 13 deletions modules/nf-core/calder2/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@ process CALDER2 {
output:
tuple val(meta), path("${prefix}/") , emit: output_folder
tuple val(meta), path("${prefix}/intermediate_data/") , emit: intermediate_data_folder , optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('calder'), val('0.7'), emit: versions_calder, topic: versions
// WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.

when:
task.ext.when == null || task.ext.when
Expand All @@ -26,7 +27,6 @@ process CALDER2 {
prefix = task.ext.prefix ?: "${meta.id}"
def suffix = resolution ? "::/resolutions/$resolution" : ""
def cpus = task.cpus ?: 1
def VERSION = '0.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
# getting binsize as mandatory input for calder
binsize="\$(cooler info --field bin-size $cool$suffix)"
Expand All @@ -37,16 +37,10 @@ process CALDER2 {
--type cool \\
--bin_size "\${binsize}" \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
calder: $VERSION
END_VERSIONS
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '0.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
mkdir -p ${prefix}/sub_compartments
mkdir -p ${prefix}/sub_domains
Expand All @@ -58,10 +52,5 @@ process CALDER2 {
touch ${prefix}/sub_compartments/cor_with_ref.txt

touch ${prefix}/sub_domains/all_nested_boundaries.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
calder: $VERSION
END_VERSIONS
"""
}
53 changes: 34 additions & 19 deletions modules/nf-core/calder2/meta.yml
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Expand Up @@ -14,48 +14,63 @@ tools:
documentation: "https://github.com/CSOgroup/CALDER2"
tool_dev_url: "https://github.com/CSOgroup/CALDER2"
doi: "10.1038/s41467-021-22666-3"
licence: ["MIT"]
licence:
- "MIT"
identifier: ""
input:
- - meta:
type: map
description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false
]
description: Groovy Map containing sample information. E.g. [ id:'test',
single_end:false ]
- cool:
type: file
description: Path to COOL file
pattern: "*.{cool.mcool}"
ontologies: []
- resolution:
type: integer
description: In case a .mcool file is provided, which resolution level to use
for the analysis
description: In case a .mcool file is provided, which resolution level to
use for the analysis
output:
output_folder:
- - meta:
type: map
description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false
]
description: Groovy Map containing sample information. E.g. [ id:'test',
single_end:false ]
- ${prefix}/:
type: directory
description: Output folder containing sub-compartment (.tsv/.bed) and domain
boundaries calls (.bed)
description: Output folder containing sub-compartment (.tsv/.bed) and
domain boundaries calls (.bed)
intermediate_data_folder:
- - meta:
type: map
description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false
]
description: Groovy Map containing sample information. E.g. [ id:'test',
single_end:false ]
- ${prefix}/intermediate_data/:
type: directory
description: Output folder containing intermediate data produced during the
computation
description: Output folder containing intermediate data produced during
the computation
versions_calder:
- - ${task.process}:
type: string
description: The name of the process
- calder:
type: string
description: The name of the tool
- "0.7":
type: string
description: The expression to obtain the version of the tool
topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The name of the process
- calder:
type: string
description: The name of the tool
- "0.7":
type: string
description: The expression to obtain the version of the tool
authors:
- "@lucananni93"
maintainers:
Expand Down
4 changes: 2 additions & 2 deletions modules/nf-core/calder2/tests/main.nf.test
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Expand Up @@ -52,7 +52,7 @@ nextflow_process {
assert snapshot(
all_file_names,
stable_files,
process.out.versions[0]
process.out.versions_calder[0]
).match()
}
)
Expand Down Expand Up @@ -100,7 +100,7 @@ nextflow_process {
assert snapshot(
all_file_names,
stable_files,
process.out.versions[0]
process.out.versions_calder[0]
).match()
}
)
Expand Down
52 changes: 37 additions & 15 deletions modules/nf-core/calder2/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,11 @@

],
"2": [
"versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0"
[
"CALDER2",
"calder",
"0.7"
]
],
"intermediate_data_folder": [

Expand All @@ -49,16 +53,20 @@
]
]
],
"versions": [
"versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0"
"versions_calder": [
[
"CALDER2",
"calder",
"0.7"
]
]
}
],
"timestamp": "2026-03-13T10:44:04.45799756",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-02T15:17:11.435944"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
}
},
"test-calder2-cool": {
"content": [
Expand All @@ -77,13 +85,20 @@
"cor_with_ref.txt:md5,54f954d92df161db5cae7845d2786ad2",
"all_nested_boundaries.bed:md5,56172ee755f573ad57320273ca0f52cd"
],
"versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0"
[
"CALDER2",
"calder",
"0.7"
]
],
"timestamp": "2026-03-13T10:24:39.4710294",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
},
"timestamp": "2024-09-02T15:16:37.504391"
"versions_calder": [
["CALDER2", "calder", "0.7"]
]
},
"test-calder2-mcool": {
"content": [
Expand All @@ -102,12 +117,19 @@
"cor_with_ref.txt:md5,f748876d367d0fdb751bd00e8e9bf60a",
"all_nested_boundaries.bed:md5,c066de5e2e789e3fe65b900a3b0a4876"
],
"versions.yml:md5,b312ffd67c18a79a5db11b78777c00d0"
[
"CALDER2",
"calder",
"0.7"
]
],
"timestamp": "2026-03-13T10:26:07.222064175",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
"nf-test": "0.9.4",
"nextflow": "25.10.4"
},
"timestamp": "2024-09-02T15:17:06.081233"
"versions_calder": [
["CALDER2", "calder", "0.7"]
]
}
}
4 changes: 4 additions & 0 deletions modules/nf-core/calder2/tests/nextflow.config
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@@ -1,3 +1,7 @@
process {
ext.args = '--genome hg38'
}
singularity {
enabled = true
pullTimeout = '1h'
}
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