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Update module BFTOOLS/SHOWINF: Changed for compressed output #9797

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AlexBarbera wants to merge 4 commits into from
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Update module BFTOOLS/SHOWINF: Changed for compressed output #9797

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2ebd080
Changed for compressed output
AlexBarbera Jan 28, 2026
1796240
Fixed file suffixes
AlexBarbera Jan 28, 2026
78a6131
fix unavailable gzip version
AlexBarbera Feb 2, 2026
b5fe074
updated meta to match compressed output
AlexBarbera Feb 2, 2026
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8 changes: 4 additions & 4 deletions modules/nf-core/bftools/showinf/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ process BFTOOLS_SHOWINF {
tuple val(meta), path(image)

output:
tuple val(meta), path("*.xml"), emit: xml
path "versions.yml" , emit: versions
tuple val(meta), path("*.xml.gz"), emit: xml
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -25,7 +25,7 @@ process BFTOOLS_SHOWINF {
export BF_FLAGS='-XX:+PerfDisableSharedMem'
showinf -nopix -no-upgrade -omexml-only \\
$args \\
$image > ${prefix}.xml
$image | gzip > ${prefix}.xml.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -38,7 +38,7 @@ process BFTOOLS_SHOWINF {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
echo '<?xml version="1.0" encoding="UTF-8">' > ${prefix}.xml
echo '<?xml version="1.0" encoding="UTF-8">' | gzip > ${prefix}.xml.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
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4 changes: 2 additions & 2 deletions modules/nf-core/bftools/showinf/meta.yml
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Expand Up @@ -32,9 +32,9 @@ output:
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- "*.xml":
- "*.xml.gz":
type: file
description: XML with OME tag metadata
description: Compressed XML with OME tag metadata
ontologies:
- edam: "http://edamontology.org/format_2332" # XML

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2 changes: 1 addition & 1 deletion modules/nf-core/bftools/showinf/tests/main.nf.test
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Expand Up @@ -13,7 +13,7 @@ nextflow_process {
when {
process {
"""
input[0] = [["id":0], file(params.modules_testdata_base_path + "/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif")]
input[0] = [["id":0], file(params.modules_testdata_base_path + "imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif", checkIfExists: true)]
"""
}
}
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18 changes: 9 additions & 9 deletions modules/nf-core/bftools/showinf/tests/main.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
{
"id": 0
},
"0.xml:md5,b4e08d86595e773c42483343b06cd51d"
"0.xml.gz:md5,b4e08d86595e773c42483343b06cd51d"
]
],
"1": [
Expand All @@ -21,16 +21,16 @@
{
"id": 0
},
"0.xml:md5,b4e08d86595e773c42483343b06cd51d"
"0.xml.gz:md5,b4e08d86595e773c42483343b06cd51d"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.1"
"nextflow": "25.10.3"
},
"timestamp": "2025-07-02T16:38:33.421740218"
"timestamp": "2026-02-02T12:24:28.660967528"
},
"ometif - stub": {
"content": [
Expand All @@ -40,7 +40,7 @@
{
"id": 0
},
"0.xml:md5,7a28b7ee02f003b473412feef56fb859"
"0.xml.gz:md5,7a28b7ee02f003b473412feef56fb859"
]
],
"1": [
Expand All @@ -54,15 +54,15 @@
{
"id": 0
},
"0.xml:md5,7a28b7ee02f003b473412feef56fb859"
"0.xml.gz:md5,7a28b7ee02f003b473412feef56fb859"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.1"
"nextflow": "25.10.3"
},
"timestamp": "2025-07-02T16:38:36.416535453"
"timestamp": "2026-02-02T12:24:33.598126172"
}
}
}
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