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Mirtrace topics migration #12183

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71586ed
Update module
EfraMP Jun 26, 2026
91c1b8f
Solve bug
EfraMP Jun 26, 2026
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34 changes: 12 additions & 22 deletions modules/nf-core/mirtrace/qc/main.nf
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Original file line number Diff line number Diff line change
@@ -1,29 +1,29 @@
process MIRTRACE_QC {
tag "$meta.id"
tag "${meta.id}"
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mirtrace:1.0.1--0':
'quay.io/biocontainers/mirtrace:1.0.1--0' }"
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/mirtrace:1.0.1--0'
: 'quay.io/biocontainers/mirtrace:1.0.1--0'}"

input:
tuple val(meta), path(reads), path(mirtrace_config)
val(mirtrace_species)
val mirtrace_species

output:
tuple val(meta), path ("*.html") , emit: html
tuple val(meta), path ("*.json") , emit: json
tuple val(meta), path ("*.tsv") , emit: tsv
tuple val(meta), path ("qc_passed_reads.all.collapsed/*.{fa,fasta}") , emit: all_fa
tuple val(meta), path ("qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}") , emit: rnatype_unknown_fa
path "versions.yml" , emit: versions
tuple val(meta), path("*.html"), emit: html
tuple val(meta), path("*.json"), emit: json
tuple val(meta), path("*.tsv"), emit: tsv
tuple val(meta), path("qc_passed_reads.all.collapsed/*.{fa,fasta}"), emit: all_fa
tuple val(meta), path("qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}"), emit: rnatype_unknown_fa
tuple val("${task.process}"), val('mirtrace'), eval('mirtrace -v'), emit: versions_mirtrace, topic: versions

when:
task.ext.when == null || task.ext.when

script:
def mirtrace_mode = mirtrace_config ? "--config ${mirtrace_config}": "${reads}"
def mirtrace_mode = mirtrace_config ? "--config ${mirtrace_config}" : "${reads}"

"""
mirtrace qc \\
Expand All @@ -32,11 +32,6 @@ process MIRTRACE_QC {
--output-dir . \\
--force \\
${mirtrace_mode}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mirtrace: \$(echo \$(mirtrace -v))
END_VERSIONS
"""

stub:
Expand All @@ -52,10 +47,5 @@ process MIRTRACE_QC {

touch qc_passed_reads.all.collapsed/${prefix}.fa
touch qc_passed_reads.rnatype_unknown.collapsed/${prefix}.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mirtrace: \$(echo \$(mirtrace -v))
END_VERSIONS
"""
}
55 changes: 34 additions & 21 deletions modules/nf-core/mirtrace/qc/meta.yml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
name: "mirtrace_qc"
description: "A tool for quality control and tracing taxonomic origins of microRNA
sequencing data"
Expand All @@ -23,9 +22,9 @@ tools:
documentation: "https://github.com/friedlanderlab/mirtrace/blob/master/release-bundle-includes/doc/manual/mirtrace_manual.pdf"
tool_dev_url: "https://github.com/friedlanderlab/mirtrace/tree/master"
doi: "10.1186/s13059-018-1588-9"
licence: ["GPL v2"]
licence:
- "GPL v2"
identifier: biotools:miRTrace

input:
- - meta:
type: map
Expand All @@ -37,17 +36,17 @@ input:
description: microRNA sequencing data
pattern: "*.{fastq,fastq.gz}"
ontologies:
- edam: http://edamontology.org/format_1930 # FASTQ
- edam: http://edamontology.org/format_1930
- mirtrace_config:
type: file
description: (Optional) CSV with list of FASTQ files to process with one entry
per row. No headers. Each row consists of the following columns "FASTQ file
path, id, adapter, PHRED-ASCII-offset".
description: (Optional) CSV with list of FASTQ files to process with one
entry per row. No headers. Each row consists of the following columns
"FASTQ file path, id, adapter, PHRED-ASCII-offset".
ontologies: []
- mirtrace_species:
type: string
description: Target species in microRNA sequencing data (miRbase encoding, e.g.
“hsa” for Homo sapiens)
description: Target species in microRNA sequencing data (miRbase encoding,
e.g. “hsa” for Homo sapiens)
output:
html:
- - meta:
Expand All @@ -71,7 +70,7 @@ output:
description: JSON file
pattern: "*.{json}"
ontologies:
- edam: http://edamontology.org/format_3464 # JSON
- edam: http://edamontology.org/format_3464
tsv:
- - meta:
type: map
Expand All @@ -83,7 +82,7 @@ output:
description: TSV file
pattern: "*.{tsv}"
ontologies:
- edam: http://edamontology.org/format_3475 # TSV
- edam: http://edamontology.org/format_3475
all_fa:
- - meta:
type: map
Expand All @@ -92,8 +91,8 @@ output:
e.g. `[ id:'sample1', single_end:false ]`
- qc_passed_reads.all.collapsed/*.{fa,fasta}:
type: file
description: QC-passed reads in FASTA file. Identical reads are collapsed.
Entries are sorted by abundance.
description: QC-passed reads in FASTA file. Identical reads are
collapsed. Entries are sorted by abundance.
pattern: "*.{fa,fasta}"
ontologies: []
rnatype_unknown_fa:
Expand All @@ -104,17 +103,31 @@ output:
e.g. `[ id:'sample1', single_end:false ]`
- qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}:
type: file
description: Unknown RNA type QC-passed reads in FASTA file. Identical reads
are collapsed. Entries are sorted by abundance.
description: Unknown RNA type QC-passed reads in FASTA file. Identical
reads are collapsed. Entries are sorted by abundance.
pattern: "*.{fa,fasta}"
ontologies: []
versions_mirtrace:
- - ${task.process}:
type: string
description: The name of the process
- mirtrace:
type: string
description: The name of the tool
- mirtrace -v:
type: eval
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
- mirtrace:
type: string
description: The name of the tool
- mirtrace -v:
type: eval
description: The expression to obtain the version of the tool
authors:
- "@atrigila"
maintainers:
Expand Down
5 changes: 4 additions & 1 deletion modules/nf-core/mirtrace/qc/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ nextflow_process {
{ assert snapshot(process.out.all_fa).match("all_fa") },

// Check versions
{ assert snapshot(process.out.versions).match("versions") }
{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("versions") },

)
}
Expand Down Expand Up @@ -121,6 +121,9 @@ nextflow_process {
{ assert snapshot(process.out.rnatype_unknown_fa).match("rnatype_unknown_fa_config") },
{ assert snapshot(process.out.all_fa).match("all_fa_config") },

// Check versions
{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match("versions_config") },

)
}

Expand Down
94 changes: 63 additions & 31 deletions modules/nf-core/mirtrace/qc/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@
]
]
],
"timestamp": "2024-09-10T18:35:10.022991825",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-10T18:35:10.022991825"
}
},
"all_fa": {
"content": [
Expand All @@ -28,23 +28,11 @@
]
]
],
"timestamp": "2024-09-10T18:33:02.971744888",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-10T18:33:02.971744888"
},
"versions": {
"content": [
[
"versions.yml:md5,b50529beb497fc9882232140b636d9ce"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-02T14:00:50.712738593"
}
},
"tsv_config": {
"content": [
Expand All @@ -65,11 +53,29 @@
]
]
],
"timestamp": "2024-09-10T18:35:09.99291948",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-10T18:35:09.99291948"
}
},
"versions": {
"content": [
{
"versions_mirtrace": [
[
"MIRTRACE_QC",
"mirtrace",
"1.0.1"
]
]
}
],
"timestamp": "2026-06-26T17:01:42.471329",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.04.1"
}
},
"tsv": {
"content": [
Expand All @@ -91,11 +97,11 @@
]
]
],
"timestamp": "2024-09-10T18:33:02.856967195",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-10T18:33:02.856967195"
}
},
"rnatype_unknown_fa_config": {
"content": [
Expand All @@ -108,11 +114,29 @@
]
]
],
"timestamp": "2024-09-10T18:35:10.010723637",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-10T18:35:10.010723637"
}
},
"versions_config": {
"content": [
{
"versions_mirtrace": [
[
"MIRTRACE_QC",
"mirtrace",
"1.0.1"
]
]
}
],
"timestamp": "2026-06-26T17:03:42.424407",
"meta": {
"nf-test": "0.9.4",
"nextflow": "26.04.1"
}
},
"human - fastq - stub": {
"content": [
Expand Down Expand Up @@ -163,7 +187,11 @@
]
],
"5": [
"versions.yml:md5,b50529beb497fc9882232140b636d9ce"
[
"MIRTRACE_QC",
"mirtrace",
"1.0.1"
]
],
"all_fa": [
[
Expand Down Expand Up @@ -210,16 +238,20 @@
"test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,b50529beb497fc9882232140b636d9ce"
"versions_mirtrace": [
[
"MIRTRACE_QC",
"mirtrace",
"1.0.1"
]
]
}
],
"timestamp": "2026-06-26T16:40:20.531125",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-02T13:43:42.209949119"
"nf-test": "0.9.4",
"nextflow": "26.04.1"
}
},
"rnatype_unknown_fa": {
"content": [
Expand All @@ -233,10 +265,10 @@
]
]
],
"timestamp": "2024-09-10T18:33:02.917439516",
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-10T18:33:02.917439516"
}
}
}
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