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Merged
dialvarezs merged 4 commits into from
Dec 8, 2025
Merged

semibin/singleeasybin: bump version + migrate to topics #9517

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0beba30
Update semibin2 module
dialvarezs Dec 7, 2025
8b0cdc9
Update snapshot
dialvarezs Dec 7, 2025
6f367bb
Remove unneeded snapshot section
dialvarezs Dec 8, 2025
98ed098
Merge branch 'master' into update-semibin
mashehu Dec 8, 2025
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5 changes: 1 addition & 4 deletions modules/nf-core/semibin/singleeasybin/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::semibin=2.2.0
# This pins solves an issue of SemiBin getting stuck.
# See https://github.com/BigDataBiology/SemiBin/issues/208
- conda-forge::igraph=0.10.17
- bioconda::semibin=2.2.1
37 changes: 14 additions & 23 deletions modules/nf-core/semibin/singleeasybin/main.nf
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Original file line number Diff line number Diff line change
@@ -1,21 +1,21 @@
process SEMIBIN_SINGLEEASYBIN {
tag "$meta.id"
tag "${meta.id}"
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/0d/0d205dadfeb5d37829b4fbde39319b07e2971884670ff7e84df4cc4d809ff8a5/data':
'community.wave.seqera.io/library/semibin_igraph:fcb667d6c87bf3fd' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2aa21f74001110a50915b90b72aca51c1e2c804ce45d686e6f4085efa69f8a5b/data'
: 'community.wave.seqera.io/library/semibin:2.2.1--3214db8e39e5117b'}"

input:
tuple val(meta), path(fasta), path(bam)

output:
tuple val(meta), path("${prefix}/*.csv") , emit: csv
tuple val(meta), path("${prefix}/*.h5") , emit: model, optional: true
tuple val(meta), path("${prefix}/*.tsv") , emit: tsv
tuple val(meta), path("${prefix}/output_bins/*.fa.gz"), emit: output_fasta
path "versions.yml", emit: versions
tuple val(meta), path("${prefix}/*.csv") , emit: csv
tuple val(meta), path("${prefix}/*.h5") , emit: model , optional: true
tuple val(meta), path("${prefix}/*.tsv") , emit: tsv
tuple val(meta), path("${prefix}/output_bins/*.fa.gz") , emit: output_fasta
tuple val("${task.process}"), val('SemiBin'), eval("SemiBin2 --version"), emit: versions_semibin, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -27,32 +27,23 @@ process SEMIBIN_SINGLEEASYBIN {
"""

SemiBin2 \\
$args \\
${args} \\
single_easy_bin \\
--input-fasta ${fasta} \\
--input-bam ${bam} \\
--output ${prefix} \\
-t $task.cpus \\
$args2

cat <<-END_VERSIONS > versions.yml
"${task.process}":
SemiBin: \$( SemiBin2 --version )
END_VERSIONS
-t ${task.cpus} \\
${args2}
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir ${prefix}
touch ${prefix}/{contig_bins,recluster_bins_info}.tsv
touch ${prefix}/{data,data_split}.csv
mkdir ${prefix}/output_bins
touch ${prefix}/output_bins/SemiBin_{0,1,2,3}.fa
gzip ${prefix}/output_bins/SemiBin*

cat <<-END_VERSIONS > versions.yml
"${task.process}":
SemiBin: \$( SemiBin2 --version )
END_VERSIONS
"""
}
19 changes: 12 additions & 7 deletions modules/nf-core/semibin/singleeasybin/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -76,13 +76,18 @@ output:
description: precluster fasta files
pattern: "*.fa"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions_semibin: &versions
- - ${task.process}:
type: string
description: The name of the process
- SemiBin:
type: string
description: The name of the tool
- "SemiBin2 --version":
type: eval
description: The expression to obtain the version of the tool
topics:
versions: *versions
authors:
- "@BigDataBiology"
maintainers:
Expand Down
26 changes: 10 additions & 16 deletions modules/nf-core/semibin/singleeasybin/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -21,20 +21,17 @@ nextflow_process {
process {
"""
input[0] = [
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1_contigs.sorted.bam', checkIfExists:true)
]
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1_contigs.sorted.bam', checkIfExists:true)
]
"""
}
}
then {
assert process.success
assertAll(
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match() }
)
}
}
Expand All @@ -49,20 +46,17 @@ nextflow_process {
process {
"""
input[0] = [
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1_contigs.sorted.bam', checkIfExists:true)
]
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/illumina/bam/test1_contigs.sorted.bam', checkIfExists:true)
]
"""
}
}
then {
assert process.success
assertAll(
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match() }
)
}
}
Expand Down
96 changes: 52 additions & 44 deletions modules/nf-core/semibin/singleeasybin/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@
"id": "test"
},
[
"contig_bins.tsv:md5,916794264bed0eefb53ec751c19862f0",
"recluster_bins_info.tsv:md5,271b128eac7a71a1fc95efddf07e1e3d"
"contig_bins.tsv:md5,4ca344a6afd99ec00b364998e88f8860",
"recluster_bins_info.tsv:md5,18975f1d33e4d060eae440ccf88a339b"
]
]
],
Expand All @@ -34,8 +34,8 @@
"id": "test"
},
[
"SemiBin_0.fa.gz:md5,87086957c6c48e2c7c8487e8f46153d3",
"SemiBin_1.fa.gz:md5,fbeaa0f639121a85115bc3c901be3cfe",
"SemiBin_0.fa.gz:md5,d03dbf09afa367f26b76c7cf8506a471",
"SemiBin_1.fa.gz:md5,f44ce9c34e8ed8743e82c9597dfa4d7c",
"SemiBin_10.fa.gz:md5,26d8fb83db377abef7d62d291d6dedc4",
"SemiBin_11.fa.gz:md5,caaec1412eabe5bc7099f7fe883e7998",
"SemiBin_12.fa.gz:md5,55b5482682aec7baa33c0646569f82b1",
Expand All @@ -52,21 +52,26 @@
"SemiBin_22.fa.gz:md5,c98a8752771d62d966a88fec80edc4c2",
"SemiBin_23.fa.gz:md5,c9ab00537eee994d2ad326998ddd559d",
"SemiBin_24.fa.gz:md5,039495af6b66f05d415e7de7fe0a20fb",
"SemiBin_25.fa.gz:md5,9a204ce83ea1fa70934cd0dc78953a02",
"SemiBin_26.fa.gz:md5,63750434b3295487ea7c3f747347ea18",
"SemiBin_27.fa.gz:md5,00e61d0c6a894debb626d97a7a468163",
"SemiBin_25.fa.gz:md5,679d9fbca921a242fa36c4eb58439d17",
"SemiBin_26.fa.gz:md5,9a204ce83ea1fa70934cd0dc78953a02",
"SemiBin_27.fa.gz:md5,63750434b3295487ea7c3f747347ea18",
"SemiBin_28.fa.gz:md5,00e61d0c6a894debb626d97a7a468163",
"SemiBin_3.fa.gz:md5,4730f1e32e5323283fe885884f10699e",
"SemiBin_4.fa.gz:md5,d94e4065dfb334eb34f04f4f06af648e",
"SemiBin_5.fa.gz:md5,27ad83d85184527847a2cc13b1c990b0",
"SemiBin_6.fa.gz:md5,1741f7cac38fb8c5b03600ec2fe027c0",
"SemiBin_7.fa.gz:md5,406697b0e472cf577b6b265466ab73af",
"SemiBin_8.fa.gz:md5,b9ce47f44ef95492c7cb1a578ad48b7d",
"SemiBin_4.fa.gz:md5,546de9f41e32277068eb27a18eb5455c",
"SemiBin_5.fa.gz:md5,d94e4065dfb334eb34f04f4f06af648e",
"SemiBin_6.fa.gz:md5,27ad83d85184527847a2cc13b1c990b0",
"SemiBin_7.fa.gz:md5,1741f7cac38fb8c5b03600ec2fe027c0",
"SemiBin_8.fa.gz:md5,406697b0e472cf577b6b265466ab73af",
"SemiBin_9.fa.gz:md5,f1c9b082977bf100918591b489fd03e2"
]
]
],
"4": [
"versions.yml:md5,cbc3652f97526cada170758d03959d6f"
[
"SEMIBIN_SINGLEEASYBIN",
"SemiBin",
"2.2.1"
]
],
"csv": [
[
Expand All @@ -89,8 +94,8 @@
"id": "test"
},
[
"SemiBin_0.fa.gz:md5,87086957c6c48e2c7c8487e8f46153d3",
"SemiBin_1.fa.gz:md5,fbeaa0f639121a85115bc3c901be3cfe",
"SemiBin_0.fa.gz:md5,d03dbf09afa367f26b76c7cf8506a471",
"SemiBin_1.fa.gz:md5,f44ce9c34e8ed8743e82c9597dfa4d7c",
"SemiBin_10.fa.gz:md5,26d8fb83db377abef7d62d291d6dedc4",
"SemiBin_11.fa.gz:md5,caaec1412eabe5bc7099f7fe883e7998",
"SemiBin_12.fa.gz:md5,55b5482682aec7baa33c0646569f82b1",
Expand All @@ -107,15 +112,16 @@
"SemiBin_22.fa.gz:md5,c98a8752771d62d966a88fec80edc4c2",
"SemiBin_23.fa.gz:md5,c9ab00537eee994d2ad326998ddd559d",
"SemiBin_24.fa.gz:md5,039495af6b66f05d415e7de7fe0a20fb",
"SemiBin_25.fa.gz:md5,9a204ce83ea1fa70934cd0dc78953a02",
"SemiBin_26.fa.gz:md5,63750434b3295487ea7c3f747347ea18",
"SemiBin_27.fa.gz:md5,00e61d0c6a894debb626d97a7a468163",
"SemiBin_25.fa.gz:md5,679d9fbca921a242fa36c4eb58439d17",
"SemiBin_26.fa.gz:md5,9a204ce83ea1fa70934cd0dc78953a02",
"SemiBin_27.fa.gz:md5,63750434b3295487ea7c3f747347ea18",
"SemiBin_28.fa.gz:md5,00e61d0c6a894debb626d97a7a468163",
"SemiBin_3.fa.gz:md5,4730f1e32e5323283fe885884f10699e",
"SemiBin_4.fa.gz:md5,d94e4065dfb334eb34f04f4f06af648e",
"SemiBin_5.fa.gz:md5,27ad83d85184527847a2cc13b1c990b0",
"SemiBin_6.fa.gz:md5,1741f7cac38fb8c5b03600ec2fe027c0",
"SemiBin_7.fa.gz:md5,406697b0e472cf577b6b265466ab73af",
"SemiBin_8.fa.gz:md5,b9ce47f44ef95492c7cb1a578ad48b7d",
"SemiBin_4.fa.gz:md5,546de9f41e32277068eb27a18eb5455c",
"SemiBin_5.fa.gz:md5,d94e4065dfb334eb34f04f4f06af648e",
"SemiBin_6.fa.gz:md5,27ad83d85184527847a2cc13b1c990b0",
"SemiBin_7.fa.gz:md5,1741f7cac38fb8c5b03600ec2fe027c0",
"SemiBin_8.fa.gz:md5,406697b0e472cf577b6b265466ab73af",
"SemiBin_9.fa.gz:md5,f1c9b082977bf100918591b489fd03e2"
]
]
Expand All @@ -126,26 +132,25 @@
"id": "test"
},
[
"contig_bins.tsv:md5,916794264bed0eefb53ec751c19862f0",
"recluster_bins_info.tsv:md5,271b128eac7a71a1fc95efddf07e1e3d"
"contig_bins.tsv:md5,4ca344a6afd99ec00b364998e88f8860",
"recluster_bins_info.tsv:md5,18975f1d33e4d060eae440ccf88a339b"
]
]
],
"versions": [
"versions.yml:md5,cbc3652f97526cada170758d03959d6f"
"versions_semibin": [
[
"SEMIBIN_SINGLEEASYBIN",
"SemiBin",
"2.2.1"
]
]
},
{
"SEMIBIN_SINGLEEASYBIN": {
"SemiBin": "2.2.0"
}
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-12-02T13:19:13.461592294"
"timestamp": "2025-12-08T12:07:46.964893039"
},
"bacteroides_fragilis - stub": {
"content": [
Expand Down Expand Up @@ -189,7 +194,11 @@
]
],
"4": [
"versions.yml:md5,cbc3652f97526cada170758d03959d6f"
[
"SEMIBIN_SINGLEEASYBIN",
"SemiBin",
"2.2.1"
]
],
"csv": [
[
Expand Down Expand Up @@ -229,20 +238,19 @@
]
]
],
"versions": [
"versions.yml:md5,cbc3652f97526cada170758d03959d6f"
"versions_semibin": [
[
"SEMIBIN_SINGLEEASYBIN",
"SemiBin",
"2.2.1"
]
]
},
{
"SEMIBIN_SINGLEEASYBIN": {
"SemiBin": "2.2.0"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-05-09T08:28:29.291321203"
"timestamp": "2025-12-08T12:08:04.255646853"
}
}
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