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Feat: SEQKIT_* update versions, snapshots + cleanup (#11992)
* update versions and snapshots * fix failing tests * Fix SEQKIT_REPLACE stub to only gzip .gz outputs * Standardize seqkit test files formatting and ext.args handling - Consistent nested input format with 4-space indentation - Single quotes for options '-stub' - assert process.success/process.failure before assertAll (not inside) - No trailing commas in single-item assertAll blocks - Unified ext.args config pattern: params.modules_args / params.modules_args2 - Consistent withName: SEQKIT_* (no quotes) in all config files - Removed redundant config files (fx2tab, split2 length/part/size, replace uncomp) - Consolidated split2 to single nextflow.config with per-test params * polish * Fix: move params block inside when block in all seqkit tests * Apply suggestion from @maxulysse * Standardize seqkit to v2.13.0 with community wave containers - head: 2.10.0 -> 2.13.0, biocontainers -> community wave - sana: 2.10.1 -> 2.13.0, biocontainers -> community wave - sample: fix singularity container to match other modules * snapshots * Revert "snapshots" This reverts commit 4146a83. * Reapply "snapshots" This reverts commit ebedec3. * Revert "Standardize seqkit to v2.13.0 with community wave containers" This reverts commit 4a0abd5. * Remove out_ext input from seqkit/replace - Remove val out_ext input channel - Always infer extension from input file - Remove uncomp test (depended on out_ext) * Restore uncomp test using ext.suffix instead of out_ext * fix replace * fix snapshot * typos * Standardize head and sana to seqkit 2.13.0 with community wave containers * snapshot * fix mirdeep2/mapper test * fix failing tests * fix stub * fix stub * fix failing tests * fix failing tests * fix stub test * regenerate stub tests * echo -n -> echo '' * no gunzip * | gzip properly * proper empty gz file snapshot * proper gz md5 for stub * polish * snapshot once again * restore comments
1 parent 910e3bd commit d07a945

107 files changed

Lines changed: 1213 additions & 2288 deletions

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‎modules/nf-core/mirdeep2/mapper/tests/main.nf.test‎

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@@ -45,6 +45,7 @@ nextflow_process {
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process {
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"""
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input[0] = SEQKIT_FQ2FA.out.fasta
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input[1] = 'fasta'
4849
"""
4950
}
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}

‎modules/nf-core/mirdeep2/mapper/tests/nextflow.config‎

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Original file line numberDiff line numberDiff line change
@@ -1,11 +1,9 @@
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process {
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withName: 'MIRDEEP2_MAPPER' {
2+
withName: MIRDEEP2_MAPPER {
33
ext.args = "-c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -v"
44
}
55

6-
withName: 'SEQKIT_REPLACE' {
6+
withName: SEQKIT_REPLACE {
77
ext.args = "-p '\s.+'"
8-
ext.suffix = "fasta"
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}
10-
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}

‎modules/nf-core/seqkit/concat/environment.yml‎

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@@ -4,4 +4,4 @@ channels:
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- conda-forge
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- bioconda
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dependencies:
7-
- bioconda::seqkit=2.9.0
7+
- bioconda::seqkit=2.13.0

‎modules/nf-core/seqkit/concat/main.nf‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process SEQKIT_CONCAT {
44

55
conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
7-
? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
8-
: 'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0'}"
7+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data'
8+
: 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}"
99

1010
input:
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tuple val(meta), path(input, stageAs: 'in/*')
@@ -30,8 +30,11 @@ process SEQKIT_CONCAT {
3030
"""
3131

3232
stub:
33+
def args = task.ext.args ?: ''
3334
def prefix = task.ext.prefix ?: "${meta.id}"
3435
"""
36+
echo ${args}
37+
3538
touch ${prefix}.fasta
3639
"""
3740
}

‎modules/nf-core/seqkit/concat/tests/main.nf.test‎

Lines changed: 14 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -12,22 +12,25 @@ nextflow_process {
1212

1313
test("sarscov2 and human primers - fasta") {
1414
when {
15+
params {
16+
modules_args = '--full'
17+
}
1518
process {
1619
"""
1720
input[0] = [
18-
[ id:'test' ], // meta map
21+
[ id:'test' ], // meta map
1922
[
2023
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
2124
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true)
2225
]
23-
]
26+
]
2427
"""
2528
}
2629
}
2730

2831
then {
32+
assert process.success
2933
assertAll(
30-
{ assert process.success },
3134
{ assert snapshot(
3235
file(process.out.fastx[0][1]).name,
3336
process.out.findAll { key, val -> key.startsWith('versions') }
@@ -43,27 +46,29 @@ nextflow_process {
4346
}
4447

4548
test("sarscov2 and human primers - fasta - stub") {
46-
4749
options '-stub'
4850

4951
when {
52+
params {
53+
modules_args = '--full'
54+
}
5055
process {
5156
"""
5257
input[0] = [
53-
[ id:'test' ], // meta map
54-
[
58+
[ id:'test' ], // meta map
59+
[
5560
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
5661
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fasta/primers.fasta', checkIfExists: true)
57-
]
5862
]
63+
]
5964
"""
6065
}
6166
}
6267

6368
then {
69+
assert process.success
6470
assertAll(
65-
{ assert process.success },
66-
{ assert snapshot(process.out).match()}
71+
{ assert snapshot(sanitizeOutput(process.out)).match() }
6772
)
6873
}
6974
}

‎modules/nf-core/seqkit/concat/tests/main.nf.test.snap‎

Lines changed: 8 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -7,35 +7,20 @@
77
[
88
"SEQKIT_CONCAT",
99
"seqkit",
10-
"2.9.0"
10+
"2.13.0"
1111
]
1212
]
1313
}
1414
],
15-
"timestamp": "2026-03-13T12:31:22.622460144",
15+
"timestamp": "2026-06-12T17:18:07.140936082",
1616
"meta": {
17-
"nf-test": "0.9.4",
18-
"nextflow": "25.10.4"
17+
"nf-test": "0.9.5",
18+
"nextflow": "26.04.3"
1919
}
2020
},
2121
"sarscov2 and human primers - fasta - stub": {
2222
"content": [
2323
{
24-
"0": [
25-
[
26-
{
27-
"id": "test"
28-
},
29-
"test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
30-
]
31-
],
32-
"1": [
33-
[
34-
"SEQKIT_CONCAT",
35-
"seqkit",
36-
"2.9.0"
37-
]
38-
],
3924
"fastx": [
4025
[
4126
{
@@ -48,15 +33,15 @@
4833
[
4934
"SEQKIT_CONCAT",
5035
"seqkit",
51-
"2.9.0"
36+
"2.13.0"
5237
]
5338
]
5439
}
5540
],
56-
"timestamp": "2026-03-12T12:55:48.595365683",
41+
"timestamp": "2026-06-12T17:24:13.961063008",
5742
"meta": {
58-
"nf-test": "0.9.4",
59-
"nextflow": "25.10.4"
43+
"nf-test": "0.9.5",
44+
"nextflow": "26.04.3"
6045
}
6146
}
6247
}

‎modules/nf-core/seqkit/concat/tests/nextflow.config‎

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
process {
22
withName: SEQKIT_CONCAT {
3-
ext.args = "--full"
3+
ext.args = params.modules_args ?: ''
44
}
55
}

‎modules/nf-core/seqkit/fq2fa/environment.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,4 +4,4 @@ channels:
44
- conda-forge
55
- bioconda
66
dependencies:
7-
- bioconda::seqkit=2.9.0
7+
- bioconda::seqkit=2.13.0

‎modules/nf-core/seqkit/fq2fa/main.nf‎

Lines changed: 10 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
process SEQKIT_FQ2FA {
2-
tag "$meta.id"
2+
tag "${meta.id}"
33
label 'process_single'
44

55
conda "${moduleDir}/environment.yml"
6-
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
8-
'quay.io/biocontainers/seqkit:2.9.0--h9ee0642_0' }"
6+
container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
7+
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fe272ab9a519cf418160471a485b5ef50ea3f571a8e4555a826f70a4d8243ae/data'
8+
: 'community.wave.seqera.io/library/seqkit:2.13.0--05c0a96bf9fb2751'}"
99

1010
input:
1111
tuple val(meta), path(fastq)
@@ -20,19 +20,21 @@ process SEQKIT_FQ2FA {
2020
script:
2121
def args = task.ext.args ?: ''
2222
def prefix = task.ext.prefix ?: "${meta.id}"
23-
2423
"""
2524
seqkit \\
2625
fq2fa \\
27-
$args \\
28-
-j $task.cpus \\
26+
${args} \\
27+
-j ${task.cpus} \\
2928
-o ${prefix}.fa.gz \\
30-
$fastq
29+
${fastq}
3130
"""
3231

3332
stub:
33+
def args = task.ext.args ?: ''
3434
def prefix = task.ext.prefix ?: "${meta.id}"
3535
"""
36+
echo ${args}
37+
3638
echo "" | gzip > ${prefix}.fa.gz
3739
"""
3840
}

‎modules/nf-core/seqkit/fq2fa/tests/main.nf.test‎

Lines changed: 11 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -10,47 +10,44 @@ nextflow_process {
1010
tag "seqkit/fq2fa"
1111

1212
test("sarscov2 - bam") {
13-
1413
when {
1514
process {
1615
"""
17-
input[0] = [[ id:'test', single_end:false ], // meta map
18-
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
16+
input[0] = [
17+
[ id:'test', single_end:false ], // meta map
18+
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
1919
]
2020
"""
2121
}
2222
}
2323

2424
then {
25+
assert process.success
2526
assertAll(
26-
{ assert process.success },
27-
{ assert snapshot(process.out).match() }
27+
{ assert snapshot(sanitizeOutput(process.out)).match() }
2828
)
2929
}
30-
3130
}
3231

3332
test("sarscov2 - bam - stub") {
34-
35-
options "-stub"
33+
options '-stub'
3634

3735
when {
3836
process {
3937
"""
40-
input[0] = [[ id:'test', single_end:false ], // meta map
41-
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
38+
input[0] = [
39+
[ id:'test', single_end:false ], // meta map
40+
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
4241
]
4342
"""
4443
}
4544
}
4645

4746
then {
47+
assert process.success
4848
assertAll(
49-
{ assert process.success },
50-
{ assert snapshot(process.out).match() }
49+
{ assert snapshot(sanitizeOutput(process.out)).match() }
5150
)
5251
}
53-
5452
}
55-
5653
}

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