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Update GNU sort to comply to nf-core guidelines #11072

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5666808
Move ext.suffix to input
mahesh-panchal Mar 27, 2026
76ed3c0
Update tests to unify config
mahesh-panchal Mar 27, 2026
49e9a30
Update test to use corrected input
mahesh-panchal Mar 27, 2026
fbed308
Merge branch 'master' into fix/gnu-sort-ext-compliance
mahesh-panchal Mar 30, 2026
d783cb4
Add suffix to GNU SORT input
mahesh-panchal Mar 30, 2026
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6 changes: 1 addition & 5 deletions modules/nf-core/gnu/sort/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ process GNU_SORT {
'biocontainers/coreutils:9.5' }"

input:
tuple val(meta), path(input)
tuple val(meta), path(input), val(suffix)

output:
tuple val(meta), path( "${output_file}" ) , emit: sorted
Expand All @@ -20,21 +20,17 @@ process GNU_SORT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
suffix = task.ext.suffix ?: "${input.extension}"
output_file = "${prefix}.${suffix}"
if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
sort ${args} ${input} > ${output_file}

"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
suffix = task.ext.suffix ?: "${input.extension}"
output_file = "${prefix}.${suffix}"
if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
touch ${output_file}

"""
}
3 changes: 3 additions & 0 deletions modules/nf-core/gnu/sort/meta.yml
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Expand Up @@ -28,6 +28,9 @@ input:
description: Draft assembly file
pattern: "*.{txt,bed,interval,genome,bins}"
ontologies: []
- suffix:
type: string
description: Output suffix
output:
sorted:
- - meta:
Expand Down
30 changes: 22 additions & 8 deletions modules/nf-core/gnu/sort/tests/main.nf.test
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Expand Up @@ -10,14 +10,17 @@ nextflow_process {
tag "gnu/sort"

test("unsorted_genome_sort") {
config "./sort_simple_bed.config"

when {
params {
gnu_sort_args = "-k1,1 -k2,2n"
}
process {
"""
input[0] = [
[id:'genome_test'],
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.genome', checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.genome', checkIfExists: true),
"genome.sorted"
]
"""
}
Expand All @@ -33,13 +36,17 @@ nextflow_process {
}

test("unsorted_intervals_sort") {
config "./sort_simple_bed.config"

when {
params {
gnu_sort_args = "-k1,1 -k2,2n"
}
process {
"""
input[0] = [
[id:'test'],
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.bed', checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.bed', checkIfExists: true),
"bed.sorted"
]
"""
}
Expand All @@ -55,14 +62,17 @@ nextflow_process {
}

test("unsorted_csv_sort") {
config "./sort_complex.config"

when {
params {
gnu_sort_args = "-t ';' -g -k 1,1 -k 2,2"
}
process {
"""
input[0] = [
[id:'test'],
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true),
"csv.sorted"
]
"""
}
Expand All @@ -78,15 +88,19 @@ nextflow_process {
}

test("unsorted_csv_sort_stub") {
config "./sort_complex.config"

options "-stub"

when {
params {
gnu_sort_args = "-t ';' -g -k 1,1 -k 2,2"
}
process {
"""
input[0] = [
[id:'test'],
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true)
file(params.modules_testdata_base_path + 'generic/unsorted_data/unsorted_text/test.csv', checkIfExists: true),
"csv.sorted"
]
"""
}
Expand Down
20 changes: 10 additions & 10 deletions modules/nf-core/gnu/sort/tests/main.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
{
"id": "test"
},
"test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d"
"test.csv.sorted:md5,797450743dae151378fa5b7a9b5f38cc"
]
],
"1": [
Expand All @@ -22,7 +22,7 @@
{
"id": "test"
},
"test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d"
"test.csv.sorted:md5,797450743dae151378fa5b7a9b5f38cc"
]
],
"versions_coreutils": [
Expand All @@ -35,10 +35,10 @@
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nf-test": "0.9.2",
"nextflow": "25.10.4"
},
"timestamp": "2026-01-23T15:48:28.77537237"
"timestamp": "2026-03-27T16:25:51.135939"
},
"unsorted_csv_sort_stub": {
"content": [
Expand Down Expand Up @@ -89,7 +89,7 @@
{
"id": "genome_test"
},
"genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048"
"genome_test.genome.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048"
]
],
"1": [
Expand All @@ -104,7 +104,7 @@
{
"id": "genome_test"
},
"genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048"
"genome_test.genome.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048"
]
],
"versions_coreutils": [
Expand All @@ -117,10 +117,10 @@
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nf-test": "0.9.2",
"nextflow": "25.10.4"
},
"timestamp": "2026-01-23T15:47:54.290932481"
"timestamp": "2026-03-27T16:25:43.198666"
},
"unsorted_intervals_sort": {
"content": [
Expand Down
5 changes: 5 additions & 0 deletions modules/nf-core/gnu/sort/tests/nextflow.config
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@@ -0,0 +1,5 @@
process {
withName: GNU_SORT {
ext.args = params.gnu_sort_args
}
}
6 changes: 0 additions & 6 deletions modules/nf-core/gnu/sort/tests/sort_complex.config
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6 changes: 0 additions & 6 deletions modules/nf-core/gnu/sort/tests/sort_simple_bed.config
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6 changes: 0 additions & 6 deletions modules/nf-core/gnu/sort/tests/sort_simple_genome.config
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3 changes: 2 additions & 1 deletion modules/nf-core/ultra/align/tests/main.nf.test
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Expand Up @@ -34,7 +34,8 @@ nextflow_process {
"""
input[0] = [
[id: 'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists:true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists:true),
"gtf"
]
"""
}
Expand Down
3 changes: 2 additions & 1 deletion modules/nf-core/ultra/index/tests/main.nf.test
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Expand Up @@ -20,7 +20,8 @@ nextflow_process {
"""
input[0] = [
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists:true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists:true),
"gtf"
]
"""
}
Expand Down