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Merged
LouisLeNezet merged 1 commit into from
Jun 21, 2026
Merged

Update to topic mafft/* #12110

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11 changes: 4 additions & 7 deletions modules/nf-core/mafft/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ process MAFFT_ALIGN {

output:
tuple val(meta), path("*.fas{.gz,}"), emit: fas
tuple val("${task.process}"), val("mafft"), eval("mafft --version 2>&1 | sed 's/ (.*) //g'"), topic: versions, emit: versions_mafft
tuple val("${task.process}"), val("mafft"), eval("mafft --version 2>&1 | sed 's/v//;s/ .*//'"), topic: versions, emit: versions_mafft
tuple val("${task.process}"), val("pigz"), eval("pigz --version 2>&1 | sed 's/pigz //g'") , topic: versions, emit: versions_pigz

when:
Expand Down Expand Up @@ -49,14 +49,11 @@ process MAFFT_ALIGN {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$fasta" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!"
if ("${fasta}" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!"
"""
echo ${args}

if [[ "$compress" == "true" ]]; then
echo "" | pigz -cp ${task.cpus} > ${prefix}.fas.gz
if [[ "${compress}" == "true" ]]; then
echo "" | gzip > ${prefix}.fas.gz
else
touch ${prefix}.fas
fi
Expand Down
50 changes: 27 additions & 23 deletions modules/nf-core/mafft/align/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,14 @@ keywords:
- multiple sequence alignment
tools:
- "mafft":
description: Multiple alignment program for amino acid or nucleotide sequences
based on fast Fourier transform
description: Multiple alignment program for amino acid or nucleotide
sequences based on fast Fourier transform
homepage: https://mafft.cbrc.jp/alignment/software/
documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
doi: "10.1093/nar/gkf436"
licence: ["BSD"]
licence:
- "BSD"
identifier: biotools:MAFFT
- "pigz":
description: "Parallel implementation of the gzip algorithm."
Expand All @@ -27,8 +28,8 @@ input:
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: FASTA file containing the sequences to align. May be gzipped or
uncompressed.
description: FASTA file containing the sequences to align. May be gzipped
or uncompressed.
pattern: "*.{fa,fasta}{.gz,}"
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
Expand All @@ -40,8 +41,8 @@ input:
e.g. [ id:'test', single_end:false ]
- add:
type: file
description: FASTA file containing sequences to align to the sequences in `fasta`
using `--add`. May be gzipped or uncompressed.
description: FASTA file containing sequences to align to the sequences in
`fasta` using `--add`. May be gzipped or uncompressed.
pattern: "*.{fa,fasta}{.gz,}"
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
Expand All @@ -53,8 +54,8 @@ input:
e.g. [ id:'test', single_end:false ]
- addfragments:
type: file
description: FASTA file containing sequences to align to the sequences in `fasta`
using `--addfragments`. May be gzipped or uncompressed.
description: FASTA file containing sequences to align to the sequences in
`fasta` using `--addfragments`. May be gzipped or uncompressed.
pattern: "*.{fa,fasta}{.gz,}"
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
Expand All @@ -66,8 +67,8 @@ input:
e.g. [ id:'test', single_end:false ]
- addfull:
type: file
description: FASTA file containing sequences to align to the sequences in `fasta`
using `--addfull`. May be gzipped or uncompressed.
description: FASTA file containing sequences to align to the sequences in
`fasta` using `--addfull`. May be gzipped or uncompressed.
pattern: "*.{fa,fasta}{.gz,}"
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
Expand All @@ -79,8 +80,8 @@ input:
e.g. [ id:'test', single_end:false ]
- addprofile:
type: file
description: FASTA file containing sequences to align to the sequences in `fasta`
using `--addprofile`. May be gzipped or uncompressed.
description: FASTA file containing sequences to align to the sequences in
`fasta` using `--addprofile`. May be gzipped or uncompressed.
pattern: "*.{fa,fasta}{.gz,}"
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
Expand All @@ -92,17 +93,17 @@ input:
e.g. [ id:'test', single_end:false ]
- addlong:
type: file
description: FASTA file containing sequences to align to the sequences in `fasta`
using `--addlong`. May be gzipped or uncompressed.
description: FASTA file containing sequences to align to the sequences in
`fasta` using `--addlong`. May be gzipped or uncompressed.
pattern: "*.{fa,fasta}{.gz,}"
ontologies:
- edam: http://edamontology.org/format_1919 # SEQUENCE-LIKE
- edam: http://edamontology.org/format_1929 # FASTA
- compress:
type: boolean
description: Flag representing whether the output MSA should be compressed. Set
to true to enable/false to disable compression. Compression is done using pigz,
and is multithreaded.
description: Flag representing whether the output MSA should be compressed.
Set to true to enable/false to disable compression. Compression is done
using pigz, and is multithreaded.
output:
fas:
- - meta:
Expand All @@ -112,7 +113,8 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.fas{.gz,}":
type: file
description: Aligned sequences in FASTA format. May be gzipped or uncompressed.
description: Aligned sequences in FASTA format. May be gzipped or
uncompressed.
pattern: "*.fas{.gz,}"
ontologies:
- edam: http://edamontology.org/format_2554 # ALIGNMENT FORMAT TXT
Expand All @@ -125,9 +127,10 @@ output:
- mafft:
type: string
description: The tool name
- mafft --version 2>&1 | sed 's/ (.*) //g':
- mafft --version 2>&1 | sed 's/v//;s/ .*//':
type: eval
description: The tool version
description: The expression to obtain the version of the tool

versions_pigz:
- - ${task.process}:
type: string
Expand All @@ -147,9 +150,10 @@ topics:
- mafft:
type: string
description: The tool name
- mafft --version 2>&1 | sed 's/ (.*) //g':
- mafft --version 2>&1 | sed 's/v//;s/ .*//':
type: eval
description: The tool version
description: The expression to obtain the version of the tool

- - ${task.process}:
type: string
description: The process name
Expand Down
54 changes: 27 additions & 27 deletions modules/nf-core/mafft/align/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
]
input[1] = [[:], []]
Expand All @@ -29,7 +29,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -40,7 +40,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
]
input[1] = [[:], []]
Expand All @@ -56,7 +56,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -68,10 +68,10 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [[ id:'test', single_end:false ], // meta map
input[1] = [[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
]
input[2] = [[:], []]
Expand All @@ -86,7 +86,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -97,12 +97,12 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [[:], []]
input[2] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
]
input[3] = [[:], []]
Expand All @@ -116,7 +116,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -127,12 +127,12 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [[:], []]
input[2] = [[:], []]
input[3] = [[ id:'test', single_end:false ], // meta map
input[3] = [[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
]
input[4] = [[:], []]
Expand All @@ -145,7 +145,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -157,13 +157,13 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [[:], []]
input[2] = [[:], []]
input[3] = [[:], []]
input[4] = [[ id:'test', single_end:false ], // meta map
input[4] = [[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
]
input[5] = [[:], []]
Expand All @@ -175,7 +175,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -187,15 +187,15 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [[:], []]
input[2] = [[:], []]
input[3] = [[:], []]
input[4] = [[:], []]
input[5] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
]
input[6] = true
Expand All @@ -206,7 +206,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -218,15 +218,15 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
]
input[1] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true)
]
input[2] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true)
]
input[3] = [[:], []]
Expand All @@ -240,7 +240,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -254,7 +254,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
]
input[1] = [[:], []]
Expand All @@ -270,7 +270,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand All @@ -284,7 +284,7 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true)
]
input[1] = [[:], []]
Expand All @@ -300,7 +300,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand Down
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