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sainsachikosainsachiko
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Bump software versions for minimap2 modules (#11280)
Bump versions for minimap2
1 parent fcf2d1a commit 135d883

6 files changed

Lines changed: 91 additions & 91 deletions

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‎modules/nf-core/minimap2/align/environment.yml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,5 +5,5 @@ channels:
55
- bioconda
66

77
dependencies:
8-
- bioconda::minimap2=2.29
9-
- bioconda::samtools=1.21
8+
- bioconda::minimap2=2.30
9+
- bioconda::samtools=1.23.1

‎modules/nf-core/minimap2/align/main.nf‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,8 @@ process MINIMAP2_ALIGN {
55
// Note: the versions here need to match the versions used in the mulled container below and minimap2/index
66
conda "${moduleDir}/environment.yml"
77
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
8-
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/66/66dc96eff11ab80dfd5c044e9b3425f52d818847b9c074794cf0c02bfa781661/data' :
9-
'community.wave.seqera.io/library/minimap2_samtools:33bb43c18d22e29c' }"
8+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/37/37671219cfd244eb9b33db9345d3543ffd83037419a1c57f4648aace493ec2c2/data' :
9+
'community.wave.seqera.io/library/minimap2_samtools:b09096fc890429ce' }"
1010

1111
input:
1212
tuple val(meta), path(reads)

‎modules/nf-core/minimap2/align/tests/main.nf.test.snap‎

Lines changed: 72 additions & 72 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
44
[
55
"@HD\tVN:1.6\tSO:coordinate",
66
"@SQ\tSN:MT192765.1\tLN:29829",
7-
"@PG\tID:minimap2\tPN:minimap2\tVN:2.29-r1283\tCL:minimap2 -t 2 -a genome.fasta -",
8-
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.21\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index"
7+
"@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta -",
8+
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index"
99
],
1010
"5d426b9a5f5b2c54f1d7f1e4c238ae94",
1111
"test.bam.bai",
@@ -14,16 +14,16 @@
1414
[
1515
"MINIMAP2_ALIGN",
1616
"minimap2",
17-
"2.29-r1283"
17+
"2.30-r1287"
1818
]
1919
]
2020
}
2121
],
22+
"timestamp": "2026-04-23T17:26:01.315588",
2223
"meta": {
23-
"nf-test": "0.9.3",
24-
"nextflow": "25.10.2"
25-
},
26-
"timestamp": "2026-01-22T15:02:10.851485367"
24+
"nf-test": "0.9.5",
25+
"nextflow": "25.04.2"
26+
}
2727
},
2828
"sarscov2 - bam, fasta, true, 'bai', false, false - stub": {
2929
"content": [
@@ -53,7 +53,7 @@
5353
[
5454
"MINIMAP2_ALIGN",
5555
"minimap2",
56-
"2.29-r1283"
56+
"2.30-r1287"
5757
]
5858
],
5959
"bam": [
@@ -81,16 +81,16 @@
8181
[
8282
"MINIMAP2_ALIGN",
8383
"minimap2",
84-
"2.29-r1283"
84+
"2.30-r1287"
8585
]
8686
]
8787
}
8888
],
89+
"timestamp": "2026-04-23T17:26:29.211025",
8990
"meta": {
90-
"nf-test": "0.9.3",
91-
"nextflow": "25.10.2"
92-
},
93-
"timestamp": "2026-01-22T15:02:56.708796666"
91+
"nf-test": "0.9.5",
92+
"nextflow": "25.04.2"
93+
}
9494
},
9595
"sarscov2 - fastq, fasta, true, 'bai', false, false - stub": {
9696
"content": [
@@ -120,7 +120,7 @@
120120
[
121121
"MINIMAP2_ALIGN",
122122
"minimap2",
123-
"2.29-r1283"
123+
"2.30-r1287"
124124
]
125125
],
126126
"bam": [
@@ -148,16 +148,16 @@
148148
[
149149
"MINIMAP2_ALIGN",
150150
"minimap2",
151-
"2.29-r1283"
151+
"2.30-r1287"
152152
]
153153
]
154154
}
155155
],
156+
"timestamp": "2026-04-23T17:26:14.56423",
156157
"meta": {
157-
"nf-test": "0.9.3",
158-
"nextflow": "25.10.2"
159-
},
160-
"timestamp": "2026-01-22T15:02:32.614463827"
158+
"nf-test": "0.9.5",
159+
"nextflow": "25.04.2"
160+
}
161161
},
162162
"sarscov2 - fastq, fasta, false, [], false, false - stub": {
163163
"content": [
@@ -181,7 +181,7 @@
181181
[
182182
"MINIMAP2_ALIGN",
183183
"minimap2",
184-
"2.29-r1283"
184+
"2.30-r1287"
185185
]
186186
],
187187
"bam": [
@@ -203,16 +203,16 @@
203203
[
204204
"MINIMAP2_ALIGN",
205205
"minimap2",
206-
"2.29-r1283"
206+
"2.30-r1287"
207207
]
208208
]
209209
}
210210
],
211+
"timestamp": "2026-04-23T17:26:19.467028",
211212
"meta": {
212-
"nf-test": "0.9.3",
213-
"nextflow": "25.10.2"
214-
},
215-
"timestamp": "2026-01-22T15:02:40.02163098"
213+
"nf-test": "0.9.5",
214+
"nextflow": "25.04.2"
215+
}
216216
},
217217
"sarscov2 - fastq, fasta, true, [], false, false - stub": {
218218
"content": [
@@ -236,7 +236,7 @@
236236
[
237237
"MINIMAP2_ALIGN",
238238
"minimap2",
239-
"2.29-r1283"
239+
"2.30-r1287"
240240
]
241241
],
242242
"bam": [
@@ -258,74 +258,74 @@
258258
[
259259
"MINIMAP2_ALIGN",
260260
"minimap2",
261-
"2.29-r1283"
261+
"2.30-r1287"
262262
]
263263
]
264264
}
265265
],
266+
"timestamp": "2026-04-23T17:26:10.208287",
266267
"meta": {
267-
"nf-test": "0.9.3",
268-
"nextflow": "25.10.2"
269-
},
270-
"timestamp": "2026-01-22T15:02:25.102539679"
268+
"nf-test": "0.9.5",
269+
"nextflow": "25.04.2"
270+
}
271271
},
272272
"sarscov2 - [fastq1, fastq2], fasta, true, false, false": {
273273
"content": [
274274
[
275275
"@HD\tVN:1.6\tSO:coordinate",
276276
"@SQ\tSN:MT192765.1\tLN:29829",
277-
"@PG\tID:minimap2\tPN:minimap2\tVN:2.29-r1283\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz test_2.fastq.gz",
278-
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.21\tCL:samtools sort -@ 1 -o test.bam"
277+
"@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz test_2.fastq.gz",
278+
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam"
279279
],
280280
"1bc392244f228bf52cf0b5a8f6a654c9",
281281
{
282282
"versions_minimap2": [
283283
[
284284
"MINIMAP2_ALIGN",
285285
"minimap2",
286-
"2.29-r1283"
286+
"2.30-r1287"
287287
]
288288
]
289289
}
290290
],
291+
"timestamp": "2026-04-23T17:25:45.435644",
291292
"meta": {
292-
"nf-test": "0.9.3",
293-
"nextflow": "25.10.2"
294-
},
295-
"timestamp": "2026-01-22T15:01:46.456636022"
293+
"nf-test": "0.9.5",
294+
"nextflow": "25.04.2"
295+
}
296296
},
297297
"sarscov2 - fastq, fasta, true, [], false, false": {
298298
"content": [
299299
[
300300
"@HD\tVN:1.6\tSO:coordinate",
301301
"@SQ\tSN:MT192765.1\tLN:29829",
302-
"@PG\tID:minimap2\tPN:minimap2\tVN:2.29-r1283\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz",
303-
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.21\tCL:samtools sort -@ 1 -o test.bam"
302+
"@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz",
303+
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam"
304304
],
305305
"f194745c0ccfcb2a9c0aee094a08750",
306306
{
307307
"versions_minimap2": [
308308
[
309309
"MINIMAP2_ALIGN",
310310
"minimap2",
311-
"2.29-r1283"
311+
"2.30-r1287"
312312
]
313313
]
314314
}
315315
],
316+
"timestamp": "2026-04-23T17:25:35.537045",
316317
"meta": {
317-
"nf-test": "0.9.3",
318-
"nextflow": "25.10.2"
319-
},
320-
"timestamp": "2026-01-22T15:01:30.525133177"
318+
"nf-test": "0.9.5",
319+
"nextflow": "25.04.2"
320+
}
321321
},
322322
"sarscov2 - fastq, fasta, true, 'bai', false, false": {
323323
"content": [
324324
[
325325
"@HD\tVN:1.6\tSO:coordinate",
326326
"@SQ\tSN:MT192765.1\tLN:29829",
327-
"@PG\tID:minimap2\tPN:minimap2\tVN:2.29-r1283\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz",
328-
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.21\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index"
327+
"@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz",
328+
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index"
329329
],
330330
"f194745c0ccfcb2a9c0aee094a08750",
331331
"test.bam.bai",
@@ -334,41 +334,41 @@
334334
[
335335
"MINIMAP2_ALIGN",
336336
"minimap2",
337-
"2.29-r1283"
337+
"2.30-r1287"
338338
]
339339
]
340340
}
341341
],
342+
"timestamp": "2026-04-23T17:25:40.308055",
342343
"meta": {
343-
"nf-test": "0.9.3",
344-
"nextflow": "25.10.2"
345-
},
346-
"timestamp": "2026-01-22T15:01:38.84829029"
344+
"nf-test": "0.9.5",
345+
"nextflow": "25.04.2"
346+
}
347347
},
348348
"sarscov2 - bam, fasta, true, [], false, false": {
349349
"content": [
350350
[
351351
"@HD\tVN:1.6\tSO:coordinate",
352352
"@SQ\tSN:MT192765.1\tLN:29829",
353-
"@PG\tID:minimap2\tPN:minimap2\tVN:2.29-r1283\tCL:minimap2 -t 2 -a genome.fasta -",
354-
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.21\tCL:samtools sort -@ 1 -o test.bam"
353+
"@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a genome.fasta -",
354+
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam"
355355
],
356356
"5d426b9a5f5b2c54f1d7f1e4c238ae94",
357357
{
358358
"versions_minimap2": [
359359
[
360360
"MINIMAP2_ALIGN",
361361
"minimap2",
362-
"2.29-r1283"
362+
"2.30-r1287"
363363
]
364364
]
365365
}
366366
],
367+
"timestamp": "2026-04-23T17:25:55.526019",
367368
"meta": {
368-
"nf-test": "0.9.3",
369-
"nextflow": "25.10.2"
370-
},
371-
"timestamp": "2026-01-22T15:02:02.351060285"
369+
"nf-test": "0.9.5",
370+
"nextflow": "25.04.2"
371+
}
372372
},
373373
"sarscov2 - bam, fasta, true, [], false, false - stub": {
374374
"content": [
@@ -392,7 +392,7 @@
392392
[
393393
"MINIMAP2_ALIGN",
394394
"minimap2",
395-
"2.29-r1283"
395+
"2.30-r1287"
396396
]
397397
],
398398
"bam": [
@@ -414,16 +414,16 @@
414414
[
415415
"MINIMAP2_ALIGN",
416416
"minimap2",
417-
"2.29-r1283"
417+
"2.30-r1287"
418418
]
419419
]
420420
}
421421
],
422+
"timestamp": "2026-04-23T17:26:24.507384",
422423
"meta": {
423-
"nf-test": "0.9.3",
424-
"nextflow": "25.10.2"
425-
},
426-
"timestamp": "2026-01-22T15:02:47.579634041"
424+
"nf-test": "0.9.5",
425+
"nextflow": "25.04.2"
426+
}
427427
},
428428
"sarscov2 - fastq, [], true, false, false": {
429429
"content": [
@@ -529,24 +529,24 @@
529529
"@SQ\tSN:ERR5069949.3258358\tLN:151",
530530
"@SQ\tSN:ERR5069949.1476386\tLN:151",
531531
"@SQ\tSN:ERR5069949.2415814\tLN:150",
532-
"@PG\tID:minimap2\tPN:minimap2\tVN:2.29-r1283\tCL:minimap2 -t 2 -a test_1.fastq.gz test_1.fastq.gz",
533-
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.21\tCL:samtools sort -@ 1 -o test.bam"
532+
"@PG\tID:minimap2\tPN:minimap2\tVN:2.30-r1287\tCL:minimap2 -t 2 -a test_1.fastq.gz test_1.fastq.gz",
533+
"@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.23.1\tCL:samtools sort -@ 1 -o test.bam"
534534
],
535535
"16c1c651f8ec67383bcdee3c55aed94f",
536536
{
537537
"versions_minimap2": [
538538
[
539539
"MINIMAP2_ALIGN",
540540
"minimap2",
541-
"2.29-r1283"
541+
"2.30-r1287"
542542
]
543543
]
544544
}
545545
],
546+
"timestamp": "2026-04-23T17:25:49.904205",
546547
"meta": {
547-
"nf-test": "0.9.3",
548-
"nextflow": "25.10.2"
549-
},
550-
"timestamp": "2026-01-22T15:01:54.090788633"
548+
"nf-test": "0.9.5",
549+
"nextflow": "25.04.2"
550+
}
551551
}
552552
}

‎modules/nf-core/minimap2/index/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::minimap2=2.29
7+
- bioconda::minimap2=2.30

‎modules/nf-core/minimap2/index/main.nf‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@ process MINIMAP2_INDEX {
44
// Note: the versions here need to match the versions used in minimap2/align
55
conda "${moduleDir}/environment.yml"
66
container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/minimap2:2.29--h577a1d6_0' :
8-
'quay.io/biocontainers/minimap2:2.29--h577a1d6_0' }"
7+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40a39951375e148d401c77e200777053cb628a4095bda598f7d41db08cbbfa4c/data' :
8+
'community.wave.seqera.io/library/minimap2:2.30--dde6b0c5fbc82ebd' }"
99

1010
input:
1111
tuple val(meta), path(fasta)

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