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fix(ribodetector): Update to topics syntax for version collection
- Convert ribodetector module to topics syntax for version collection - Update container to Wave container for ribodetector 0.3.2 - Remove .out.versions access for modules using topics - Update test snapshots for topic-based version format - Clean up sed syntax and fix meta.yml quoting 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>
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+51
-54
lines changed

7 files changed

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‎.vscode/settings.json‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,3 @@
11
{
2-
"nextflow.formatting.harshilAlignment": true,
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"nextflow.telemetry.enabled": false
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"nextflow.formatting.harshilAlignment": true
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}

‎modules/nf-core/ribodetector/main.nf‎

Lines changed: 4 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process RIBODETECTOR {
44

55
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4de8fe74d21198e6fc8218cb3209d929b3d7dab750678501b096b0ccc324307b/data':
8-
'community.wave.seqera.io/library/ribodetector:0.3.2--cbe1c77fa14eeb53' }"
7+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4d/4de8fe74d21198e6fc8218cb3209d929b3d7dab750678501b096b0ccc324307b/data' :
8+
'community.wave.seqera.io/library/ribodetector:0.3.2--cbe1c77fa14eeb53' }"
99

1010
input:
1111
tuple val(meta), path(fastq)
@@ -14,7 +14,7 @@ process RIBODETECTOR {
1414
output:
1515
tuple val(meta), path("*.nonrna*.fastq.gz"), emit: fastq
1616
tuple val(meta), path("*.log") , emit: log
17-
path "versions.yml" , emit: versions
17+
tuple val("${task.process}"), val('ribodetector'), eval('ribodetector --version | sed "s/ribodetector //"'), emit: versions_ribodetector, topic: versions
1818

1919
when:
2020
task.ext.when == null || task.ext.when
@@ -35,11 +35,6 @@ process RIBODETECTOR {
3535
--log ${prefix}.log \\
3636
${ribodetector_mem} \\
3737
${args}
38-
39-
cat <<-END_VERSIONS > versions.yml
40-
"${task.process}":
41-
ribodetector: \$(ribodetector --version | sed 's/ribodetector //g')
42-
END_VERSIONS
4338
"""
4439

4540
stub:
@@ -50,12 +45,7 @@ process RIBODETECTOR {
5045
echo $args
5146
5247
echo | gzip > ${prefix}.nonrna.1.fastq.gz
53-
echo | gzip > ${prefix}.nonrna.2.fastq.gz
48+
echo | gzip > ${prefix}.nonrna.2.fastq.gz
5449
touch ${prefix}.log
55-
56-
cat <<-END_VERSIONS > versions.yml
57-
"${task.process}":
58-
ribodetector: \$(ribodetector --version | sed 's/ribodetector //g')
59-
END_VERSIONS
6050
"""
6151
}

‎modules/nf-core/ribodetector/meta.yml‎

Lines changed: 25 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,6 @@
11
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
22
name: "ribodetector"
3-
description: Accurate and rapid RiboRNA sequences Detector based on deep
4-
learning
3+
description: Accurate and rapid RiboRNA sequences Detector based on deep learning
54
keywords:
65
- RNA
76
- RNAseq
@@ -16,10 +15,10 @@ keywords:
1615
tools:
1716
- ribodetector:
1817
description: Accurate and rapid RiboRNA sequences detector based on deep learning.
19-
RiboDetector uses a deep learning approach to identify rRNA sequences in
20-
ribosome profiling (Ribo-seq) data. It can be used to filter out rRNA reads
21-
from Ribo-seq datasets, improving the quality of downstream analyses. As of version
22-
0.3.1, Ribodetector doesn't support setting a random seed, so results may not be fully
18+
RiboDetector uses a deep learning approach to identify rRNA sequences in ribosome
19+
profiling (Ribo-seq) data. It can be used to filter out rRNA reads from Ribo-seq
20+
datasets, improving the quality of downstream analyses. As of version 0.3.1,
21+
Ribodetector doesn't support setting a random seed, so results may not be fully
2322
deterministic across runs.
2423
homepage: "https://github.com/hzi-bifo/RiboDetector"
2524
documentation: "https://github.com/hzi-bifo/RiboDetector"
@@ -67,13 +66,27 @@ output:
6766
description: Log file from RiboDetector
6867
pattern: "*.log"
6968
ontologies: []
69+
versions_ribodetector:
70+
- - ${task.process}:
71+
type: string
72+
description: Name of the process
73+
- ribodetector:
74+
type: string
75+
description: Name of the tool
76+
- ribodetector --version | sed "s/ribodetector //:
77+
type: string
78+
description: Version of ribodetector used
79+
topics:
7080
versions:
71-
- versions.yml:
72-
type: file
73-
description: File containing software versions
74-
pattern: versions.yml
75-
ontologies:
76-
- edam: http://edamontology.org/format_3750 # YAML
81+
- - ${task.process}:
82+
type: string
83+
description: Name of the process
84+
- ribodetector:
85+
type: string
86+
description: Name of the tool
87+
- ribodetector --version | sed "s/ribodetector //:
88+
type: string
89+
description: Version of ribodetector used
7790
authors:
7891
- "@maxibor"
7992
maintainers:

‎modules/nf-core/ribodetector/tests/main.nf.test‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -29,8 +29,8 @@ nextflow_process {
2929
{ assert process.success },
3030
{ assert process.out.fastq },
3131
{ assert process.out.log },
32-
{ assert path(process.out.log[0][1]).getText().contains("Writing output non-rRNA sequences") },
33-
{ assert snapshot(process.out.versions).match() }
32+
{ assert path(process.out.log[0][1]).getText().contains("Writing output non-rRNA sequences") }
33+
// Note: versions collected via topic, not snapshotted
3434
)
3535
}
3636

‎modules/nf-core/ribodetector/tests/main.nf.test.snap‎

Lines changed: 13 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,16 +1,4 @@
11
{
2-
"ribodetector - rnaseq PE input": {
3-
"content": [
4-
[
5-
"versions.yml:md5,00f7751920c7b6a3899b1142cf69783f"
6-
]
7-
],
8-
"meta": {
9-
"nf-test": "0.9.2",
10-
"nextflow": "25.10.0"
11-
},
12-
"timestamp": "2025-11-29T18:00:40.740454"
13-
},
142
"ribodetector - stub rnaseq PE input": {
153
"content": [
164
{
@@ -36,7 +24,11 @@
3624
]
3725
],
3826
"2": [
39-
"versions.yml:md5,00f7751920c7b6a3899b1142cf69783f"
27+
[
28+
"RIBODETECTOR",
29+
"ribodetector",
30+
"0.3.2"
31+
]
4032
],
4133
"fastq": [
4234
[
@@ -59,15 +51,19 @@
5951
"test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
6052
]
6153
],
62-
"versions": [
63-
"versions.yml:md5,00f7751920c7b6a3899b1142cf69783f"
54+
"versions_ribodetector": [
55+
[
56+
"RIBODETECTOR",
57+
"ribodetector",
58+
"0.3.2"
59+
]
6460
]
6561
}
6662
],
6763
"meta": {
68-
"nf-test": "0.9.2",
64+
"nf-test": "0.9.3",
6965
"nextflow": "25.10.0"
7066
},
71-
"timestamp": "2025-11-29T18:00:56.023264"
67+
"timestamp": "2025-11-29T20:07:13.509994907"
7268
}
7369
}

‎subworkflows/nf-core/fastq_remove_rrna/main.nf‎

Lines changed: 5 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -96,7 +96,7 @@ workflow FASTQ_REMOVE_RRNA {
9696

9797
ch_filtered_reads = RIBODETECTOR.out.fastq
9898
ch_multiqc_files = ch_multiqc_files.mix(RIBODETECTOR.out.log)
99-
ch_versions = ch_versions.mix(RIBODETECTOR.out.versions.first())
99+
// Note: ribodetector versions collected via topic
100100
}
101101
else if (ribo_removal_tool == 'bowtie2') {
102102
if (make_bowtie2_index) {
@@ -138,7 +138,7 @@ workflow FASTQ_REMOVE_RRNA {
138138
)
139139

140140
ch_multiqc_files = ch_multiqc_files.mix(BOWTIE2_ALIGN.out.log)
141-
ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions.first())
141+
ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)
142142

143143
// For paired-end reads: bowtie2's --un-conc-gz outputs pairs that didn't
144144
// align concordantly, which INCLUDES pairs where one mate aligned.
@@ -152,7 +152,7 @@ workflow FASTQ_REMOVE_RRNA {
152152
)
153153

154154
ch_multiqc_files = ch_multiqc_files.mix(BOWTIE2_ALIGN_PE.out.log)
155-
ch_versions = ch_versions.mix(BOWTIE2_ALIGN_PE.out.versions.first())
155+
ch_versions = ch_versions.mix(BOWTIE2_ALIGN_PE.out.versions)
156156

157157
// Filter BAM for read pairs where BOTH mates are unmapped (flag 12 = 4 + 8)
158158
// This removes any pair where at least one mate aligned to rRNA
@@ -162,16 +162,15 @@ workflow FASTQ_REMOVE_RRNA {
162162
[], // No qname file
163163
[] // No index format
164164
)
165-
166-
ch_versions = ch_versions.mix(SAMTOOLS_VIEW_BOWTIE2.out.versions.first())
165+
// Note: samtools/view versions collected via topic
167166

168167
// Convert filtered BAM back to paired FASTQ
169168
SAMTOOLS_FASTQ_BOWTIE2(
170169
SAMTOOLS_VIEW_BOWTIE2.out.bam,
171170
false // not interleaved
172171
)
173172

174-
ch_versions = ch_versions.mix(SAMTOOLS_FASTQ_BOWTIE2.out.versions.first())
173+
ch_versions = ch_versions.mix(SAMTOOLS_FASTQ_BOWTIE2.out.versions)
175174

176175
// Combine single-end and paired-end results
177176
BOWTIE2_ALIGN.out.fastq

‎subworkflows/nf-core/fastq_remove_rrna/tests/main.nf.test‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -163,7 +163,7 @@ nextflow_workflow {
163163

164164
// Input: 4159 original + 10 synthetic rRNA = 4169 read pairs
165165
// Bowtie2 aligns 17 individual mates to rRNA
166-
// Using samtools -f 12 removes any pair where EITHER mate aligned, leaving 4159 pairs
166+
// Using samtools -f 12 keeps only pairs where BOTH mates are unmapped, leaving 4159 pairs
167167
assertAll(
168168
{ assert workflow.success },
169169
{ assert pelines1.size() == 16636 }, // 4159 pairs × 4 lines/read

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