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update bclconvert with topic #9494

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367f5c8
update bclconvert with topic
matthdsm Dec 2, 2025
cd7f378
update meta.yml
matthdsm Dec 2, 2025
939265a
Merge branch 'master' into topic/bclconvert
matthdsm Dec 3, 2025
2768511
bclconvert: move to multi stage build
matthdsm Dec 3, 2025
b783de1
update image
matthdsm Dec 3, 2025
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17 changes: 4 additions & 13 deletions modules/nf-core/bclconvert/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@ process BCLCONVERT {
tuple val(meta), path("output/**_S[1-9]*_I?_00?.fastq.gz") , emit: fastq_idx , optional:true
tuple val(meta), path("output/**Undetermined_S0*_R?_00?.fastq.gz"), emit: undetermined , optional:true
tuple val(meta), path("output/**Undetermined_S0*_I?_00?.fastq.gz"), emit: undetermined_idx, optional:true
tuple val(meta), path("output/Reports") , emit: reports
tuple val(meta), path("output/Logs") , emit: logs
tuple val(meta), path("output/InterOp/*.bin") , emit: interop , optional:true
path("versions.yml") , emit: versions
tuple val(meta), path("output/Reports/*") , emit: reports
tuple val(meta), path("output/Logs/*") , emit: logs
tuple val(meta), path("output/InterOp/*.bin") , emit: interop
tuple val("${task.process}"), val('bclconvert'), eval("bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'"), topic: versions, emit: versions_bclconvert

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -65,11 +65,6 @@ process BCLCONVERT {
# copy the InterOp folder contents to ensure it gets picked up when using fusion
mkdir -p output/InterOp/
cp -n **/InterOp/*.bin output/InterOp/

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""

stub:
Expand Down Expand Up @@ -102,10 +97,6 @@ process BCLCONVERT {
touch output/InterOp/IndexMetricsOut.bin
touch output/InterOp/QMetricsOut.bin
touch output/InterOp/TileMetricsOut.bin
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bclconvert: \$(bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //')
END_VERSIONS
"""

}
17 changes: 11 additions & 6 deletions modules/nf-core/bclconvert/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -99,13 +99,18 @@ output:
description: Interop files
pattern: "*.{bin}"
ontologies: []
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 process the versions were collected from
- bclconvert:
type: string
description: The tool name
- "bcl-convert -V 2>&1 | head -n 1 | sed 's/^.*Version //'":
type: string
description: The command used to generate the version of the tool

authors:
- "@matthdsm"
maintainers:
Expand Down
10 changes: 4 additions & 6 deletions modules/nf-core/bclconvert/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -34,12 +34,11 @@ nextflow_process {
process.out.undetermined.collect { meta, fastq -> file(fastq).name },
process.out.undetermined_idx,
process.out.reports,
process.out.logs.collect { meta, logs -> file(logs).list().sort() },
process.out.logs.collect { meta, logs -> logs.sort() },
process.out.interop.collect { meta, interop ->
interop.findAll { interopfile ->
file(interopfile).name != "IndexMetricsOut.bin" } },
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down Expand Up @@ -76,13 +75,12 @@ nextflow_process {
process.out.undetermined.collect { meta, fastq -> file(fastq).name },
process.out.undetermined_idx,
process.out.reports,
process.out.logs.collect { meta, logs -> file(logs).list().sort() },
process.out.logs.collect { meta, logs -> logs.sort() },
process.out.interop,
process.out.interop.collect { meta, interop ->
interop.findAll { interopfile ->
file(interopfile).name != "IndexMetricsOut.bin" } },
process.out.versions,
path(process.out.versions[0]).yaml
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down
74 changes: 42 additions & 32 deletions modules/nf-core/bclconvert/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,10 @@
],
[
[
"Errors.log",
"FastqComplete.txt",
"Info.log",
"Warnings.log"
"Errors.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"FastqComplete.txt:md5,081aedbb6928d0f348031f9ca49ac468",
"Info.log:md5,bec9273b64edca95b3b53c929dd8fdfc",
"Warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
[
Expand Down Expand Up @@ -92,20 +92,21 @@
"TileMetricsOut.bin:md5,21388348d81fa9be326d30ef6d348464"
]
],
[
"versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
],
{
"BCLCONVERT": {
"bclconvert": "4.4.6"
}
"versions_bclconvert": [
[
"BCLCONVERT",
"bclconvert",
"4.4.6"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-23T10:12:42.943671245"
"timestamp": "2025-12-02T14:58:16.031029"
},
"homo_sapiens illumina [bcl] - stub": {
"content": [
Expand Down Expand Up @@ -188,7 +189,11 @@
]
],
"7": [
"versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
[
"BCLCONVERT",
"bclconvert",
"4.4.6"
]
],
"fastq": [
[
Expand Down Expand Up @@ -267,16 +272,20 @@
"undetermined_idx": [

],
"versions": [
"versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
"versions_bclconvert": [
[
"BCLCONVERT",
"bclconvert",
"4.4.6"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-23T10:12:55.362214653"
"timestamp": "2025-12-02T14:30:30.75002"
},
"homo_sapiens illumina [bcl]": {
"content": [
Expand Down Expand Up @@ -323,10 +332,10 @@
],
[
[
"Errors.log",
"FastqComplete.txt",
"Info.log",
"Warnings.log"
"Errors.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"FastqComplete.txt:md5,388544f10d63d386a8d20865abf22557",
"Info.log:md5,2f3fa352080124ed5ee62afbdbc999d4",
"Warnings.log:md5,a7ec94ec82336a0e81409fe13b922f4a"
]
],
[
Expand All @@ -339,19 +348,20 @@
"TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c"
]
],
[
"versions.yml:md5,a7ddd79ad04a69cb254185a11296f1b6"
],
{
"BCLCONVERT": {
"bclconvert": "4.4.6"
}
"versions_bclconvert": [
[
"BCLCONVERT",
"bclconvert",
"4.4.6"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-23T10:12:18.369689549"
"timestamp": "2025-12-02T14:57:47.218447"
}
}
1 change: 0 additions & 1 deletion subworkflows/nf-core/bcl_demultiplex/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,6 @@ workflow BCL_DEMULTIPLEX {
ch_interop = ch_interop.mix(BCLCONVERT.out.interop)
ch_reports = ch_reports.mix(BCLCONVERT.out.reports)
ch_logs = ch_logs.mix(BCLCONVERT.out.logs)
ch_versions = ch_versions.mix(BCLCONVERT.out.versions.first())
}

// MODULE: bcl2fastq
Expand Down
15 changes: 10 additions & 5 deletions subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,12 @@
"id": "HMTFYDRXX",
"lane": 1
},
"Logs"
[
"Errors.log",
"FastqComplete.txt",
"Info.log",
"Warnings.log"
]
]
],
"reports": [
Expand Down Expand Up @@ -160,15 +165,15 @@

],
"versions": [
"versions.yml:md5,b1427a2b3abad63b04f1dd62c8f40e2e"

]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.10.0"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-11-04T16:13:41.469897018"
"timestamp": "2025-12-02T14:30:56.578335"
},
"bcl2fastq": {
"content": [
Expand Down
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