From 1376afb7efad33fc577d297c3dffd7b302ae958d Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Thu, 26 Mar 2026 20:41:24 +0000 Subject: [PATCH 01/20] topics, tests, log fixed. meta.yml needs update. lint needed --- modules/nf-core/minia/main.nf | 31 ++++--- modules/nf-core/minia/tests/main.nf.test | 41 ++++++++- modules/nf-core/minia/tests/main.nf.test.snap | 87 +++++++++++++++---- 3 files changed, 120 insertions(+), 39 deletions(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 55ff6062132c..f74beb8d2bec 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -11,10 +11,11 @@ process MINIA { tuple val(meta), path(reads) output: - tuple val(meta), path('*.contigs.fa'), emit: contigs - tuple val(meta), path('*.unitigs.fa'), emit: unitigs + tuple val(meta), path('*.contigs.fa.gz'), emit: contigs + tuple val(meta), path('*.unitigs.fa.gz'), emit: unitigs tuple val(meta), path('*.h5') , emit: h5 - path "versions.yml" , emit: versions + tuple val(meta), path("*-minia.log") , emit: log + tuple val("${task.process}"), val("minia"), eval("minia -v | grep Minia | sed 's/Minia version //g'"), topic: versions, emit: versions_minia when: task.ext.when == null || task.ext.when @@ -29,24 +30,22 @@ process MINIA { $args \\ -nb-cores $task.cpus \\ -in input_files.txt \\ - -out $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;') - END_VERSIONS + -out $prefix > ${prefix}-minia.log 2>&1 + + if [ -f ${prefix}.contigs.fa ]; then + gzip -cn ${prefix}.contigs.fa > ${prefix}.contigs.fa.gz + fi + if [ -f ${prefix}.unitigs.fa ]; then + gzip -cn ${prefix}.unitigs.fa > ${prefix}.unitigs.fa.gz + fi """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.contigs.fa - touch ${prefix}.unitigs.fa + echo "" | gzip > ${prefix}.contigs.fa.gz + echo "" | gzip > ${prefix}.unitigs.fa.gz touch ${prefix}.h5 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;') - END_VERSIONS + touch ${prefix}-minia.log """ } diff --git a/modules/nf-core/minia/tests/main.nf.test b/modules/nf-core/minia/tests/main.nf.test index e83a74c0f786..92e0b7347042 100644 --- a/modules/nf-core/minia/tests/main.nf.test +++ b/modules/nf-core/minia/tests/main.nf.test @@ -9,7 +9,39 @@ nextflow_process { tag "modules_nfcore" tag "minia" - test("test-minia") { + test("sarscov2 - fastq - se") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true), ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.contigs[0][1]).linesGzip.any { it.contains('AAA') } }, + { assert path(process.out.unitigs[0][1]).linesGzip.any { it.contains('CCC') } }, + { assert snapshot( + file(process.out.contigs[0][1]).name, + file(process.out.unitigs[0][1]).name, + file(process.out.h5[0][1]).name, + file(process.out.log[0][1]).name, + process.out.versions_minia, + ).match() + } + ) + } + } + + test("sarscov2 - fastq - pe") { when { process { @@ -29,13 +61,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert file(process.out.contigs[0][1]).text.contains('AAA') }, - { assert file(process.out.unitigs[0][1]).text.contains('CCC') }, + { assert path(process.out.contigs[0][1]).linesGzip.any { it.contains('AAA') } }, + { assert path(process.out.unitigs[0][1]).linesGzip.any { it.contains('CCC') } }, { assert snapshot( file(process.out.contigs[0][1]).name, file(process.out.unitigs[0][1]).name, file(process.out.h5[0][1]).name, - process.out.versions, + file(process.out.log[0][1]).name, + process.out.versions_minia, ).match() } ) diff --git a/modules/nf-core/minia/tests/main.nf.test.snap b/modules/nf-core/minia/tests/main.nf.test.snap index 56a728ed833b..0c85d702de7f 100644 --- a/modules/nf-core/minia/tests/main.nf.test.snap +++ b/modules/nf-core/minia/tests/main.nf.test.snap @@ -1,18 +1,43 @@ { - "test-minia": { + "sarscov2 - fastq - se": { "content": [ - "test.contigs.fa", - "test.unitigs.fa", + "test.contigs.fa.gz", + "test.unitigs.fa.gz", "test.h5", + "test-minia.log", [ - "versions.yml:md5,242f8593f9ee8955fb73580c78f30200" + [ + "MINIA", + "minia", + "3.2.5" + ] ] ], + "timestamp": "2026-03-26T20:31:46.345614709", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-05T19:56:44.252673" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 - fastq - pe": { + "content": [ + "test.contigs.fa.gz", + "test.unitigs.fa.gz", + "test.h5", + "test-minia.log", + [ + [ + "MINIA", + "minia", + "3.2.5" + ] + ] + ], + "timestamp": "2026-03-26T20:31:54.252282388", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "test-minia-stub": { "content": [ @@ -22,7 +47,7 @@ { "id": "test" }, - "test.contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.contigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -30,7 +55,7 @@ { "id": "test" }, - "test.unitigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unitigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "2": [ @@ -42,14 +67,26 @@ ] ], "3": [ - "versions.yml:md5,242f8593f9ee8955fb73580c78f30200" + [ + { + "id": "test" + }, + "test-minia.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + "MINIA", + "minia", + "3.2.5" + ] ], "contigs": [ [ { "id": "test" }, - "test.contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.contigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "h5": [ @@ -60,23 +97,35 @@ "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], + "log": [ + [ + { + "id": "test" + }, + "test-minia.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], "unitigs": [ [ { "id": "test" }, - "test.unitigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unitigs.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], - "versions": [ - "versions.yml:md5,242f8593f9ee8955fb73580c78f30200" + "versions_minia": [ + [ + "MINIA", + "minia", + "3.2.5" + ] ] } ], + "timestamp": "2026-03-26T20:36:15.351122058", "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-05T19:52:02.585904" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From 9101c917dfaf8435076b6f9456a1e6abfe939979 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 27 Mar 2026 10:52:48 +0000 Subject: [PATCH 02/20] meta.yml updated --- modules/nf-core/minia/meta.yml | 70 ++++++++++++++++++++++++---------- 1 file changed, 50 insertions(+), 20 deletions(-) diff --git a/modules/nf-core/minia/meta.yml b/modules/nf-core/minia/meta.yml index 4aeb2e124604..31e85c7f59b5 100644 --- a/modules/nf-core/minia/meta.yml +++ b/modules/nf-core/minia/meta.yml @@ -11,60 +11,90 @@ tools: a human genome on a desktop computer in a day. The output of Minia is a set of contigs. homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia - licence: ["AGPL-3.0-or-later"] + licence: + - "AGPL-3.0-or-later" identifier: biotools:minia input: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - reads: type: file description: Input reads in FastQ format pattern: "*.{fastq.gz, fastq}" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_1930 # FASTQ output: contigs: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.contigs.fa": + e.g. [ id:'test' ] + - "*.contigs.fa.gz": type: file description: The assembled contigs - pattern: "*.contigs.fa" - ontologies: [] + pattern: "*.contigs.fa.gz" + ontologies: + - edam: http://edamontology.org/format_3989 unitigs: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.unitigs.fa": + e.g. [ id:'test' ] + - "*.unitigs.fa.gz": type: file description: The assembled unitigs - pattern: "*.unitigs.fa" - ontologies: [] + pattern: "*.unitigs.fa.gz" + ontologies: + - edam: http://edamontology.org/format_3989 h5: - - meta: type: map description: | Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test' ] - "*.h5": type: file - description: Minia output h5 file - pattern: "*{.h5}" + description: Minia assembly graph in binary h5 format + pattern: "*.h5" ontologies: [] + + log: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*-minia.log": + type: file + description: Minia assembly log file + pattern: "*-minia.log" + ontologies: [] + versions_minia: + - - ${task.process}: + type: string + description: The name of the process + - minia: + type: string + description: The name of the tool + - minia -v | grep Minia | sed 's/Minia version //g': + 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 + - - ${task.process}: + type: string + description: The name of the process + - minia: + type: string + description: The name of the tool + - minia -v | grep Minia | sed 's/Minia version //g': + type: eval + description: The expression to obtain the version of the tool authors: - "@drpatelh" - "@kevinmenden" From 5c14bf14f6f02c72c373a06a157494dcfb57da98 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 27 Mar 2026 11:58:39 +0000 Subject: [PATCH 03/20] docker and singularity for some reasons contained minia 3.2.5 despite being labelled as 3.2.6 --- modules/nf-core/minia/main.nf | 10 +++---- modules/nf-core/minia/tests/main.nf.test.snap | 26 +++++++++---------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index f74beb8d2bec..4a5c0b5a29f9 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,8 +4,8 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' : - 'biocontainers/minia:3.2.6--h9a82719_0' }" + 'https://community.wave.seqera.io/library/minia:3.2.6--a3c6327b13b0c75a' : + 'community.wave.seqera.io/library/minia:3.2.6--a3c6327b13b0c75a' }" input: tuple val(meta), path(reads) @@ -13,8 +13,8 @@ process MINIA { output: tuple val(meta), path('*.contigs.fa.gz'), emit: contigs tuple val(meta), path('*.unitigs.fa.gz'), emit: unitigs - tuple val(meta), path('*.h5') , emit: h5 - tuple val(meta), path("*-minia.log") , emit: log + tuple val(meta), path('*.h5') , emit: h5 + tuple val(meta), path("*-minia.log") , emit: log tuple val("${task.process}"), val("minia"), eval("minia -v | grep Minia | sed 's/Minia version //g'"), topic: versions, emit: versions_minia when: @@ -31,7 +31,7 @@ process MINIA { -nb-cores $task.cpus \\ -in input_files.txt \\ -out $prefix > ${prefix}-minia.log 2>&1 - + if [ -f ${prefix}.contigs.fa ]; then gzip -cn ${prefix}.contigs.fa > ${prefix}.contigs.fa.gz fi diff --git a/modules/nf-core/minia/tests/main.nf.test.snap b/modules/nf-core/minia/tests/main.nf.test.snap index 0c85d702de7f..e1f76dbaec4b 100644 --- a/modules/nf-core/minia/tests/main.nf.test.snap +++ b/modules/nf-core/minia/tests/main.nf.test.snap @@ -9,15 +9,15 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ] ], - "timestamp": "2026-03-26T20:31:46.345614709", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T11:51:29.253914507" }, "sarscov2 - fastq - pe": { "content": [ @@ -29,15 +29,15 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ] ], - "timestamp": "2026-03-26T20:31:54.252282388", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T11:51:34.477805031" }, "test-minia-stub": { "content": [ @@ -78,7 +78,7 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ], "contigs": [ @@ -117,15 +117,15 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ] } ], - "timestamp": "2026-03-26T20:36:15.351122058", "meta": { - "nf-test": "0.9.4", + "nf-test": "0.9.3", "nextflow": "25.10.4" - } + }, + "timestamp": "2026-03-27T11:51:39.674097511" } } \ No newline at end of file From 080ae83bf12b8ebdbb0064cfb755ed5f4a35267f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 27 Mar 2026 12:09:22 +0000 Subject: [PATCH 04/20] [automated] Fix linting with Prettier --- modules/nf-core/minia/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/tests/main.nf.test b/modules/nf-core/minia/tests/main.nf.test index 92e0b7347042..b60a9b9315c3 100644 --- a/modules/nf-core/minia/tests/main.nf.test +++ b/modules/nf-core/minia/tests/main.nf.test @@ -40,7 +40,7 @@ nextflow_process { ) } } - + test("sarscov2 - fastq - pe") { when { From c111fc07283387762be399ae422c7e93b4e64447 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 27 Mar 2026 12:22:19 +0000 Subject: [PATCH 05/20] fix singularity --- modules/nf-core/minia/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 4a5c0b5a29f9..8ef04ff148c6 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,7 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community.wave.seqera.io/library/minia:3.2.6--a3c6327b13b0c75a' : + 'oras://community.wave.seqera.io/library/minia:3.2.6--59431d46a6352d84' : 'community.wave.seqera.io/library/minia:3.2.6--a3c6327b13b0c75a' }" input: From 352dc82fd9106945b31c80aacdac46151f2e5f63 Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Fri, 27 Mar 2026 15:38:00 +0000 Subject: [PATCH 06/20] Fix container URL for Minia process --- modules/nf-core/minia/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 8ef04ff148c6..8121c42e3b32 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,7 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/minia:3.2.6--59431d46a6352d84' : + 'https://community.wave.seqera.io/library/minia:3.2.6--59431d46a6352d84' : 'community.wave.seqera.io/library/minia:3.2.6--a3c6327b13b0c75a' }" input: From c0fff652807ab84617cf06578a114326f212247f Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Fri, 27 Mar 2026 15:50:52 +0000 Subject: [PATCH 07/20] Sorry! --- modules/nf-core/minia/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 8121c42e3b32..ea112297c4fd 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,8 +4,8 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community.wave.seqera.io/library/minia:3.2.6--59431d46a6352d84' : - 'community.wave.seqera.io/library/minia:3.2.6--a3c6327b13b0c75a' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d1/d1127b772f97ea9d62cb853d174a8e82be7e8e8598933d49b2061cb0550e276f/data' : + 'community.wave.seqera.io/library/minia:3.2.6--92bae1756baab1ef' }" input: tuple val(meta), path(reads) From 1141548ebb8546b7f1d54509e53b7471c9afcf68 Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Fri, 27 Mar 2026 15:58:26 +0000 Subject: [PATCH 08/20] Update modules/nf-core/minia/tests/main.nf.test MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/minia/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/tests/main.nf.test b/modules/nf-core/minia/tests/main.nf.test index b60a9b9315c3..a2c01ccafb71 100644 --- a/modules/nf-core/minia/tests/main.nf.test +++ b/modules/nf-core/minia/tests/main.nf.test @@ -34,7 +34,7 @@ nextflow_process { file(process.out.unitigs[0][1]).name, file(process.out.h5[0][1]).name, file(process.out.log[0][1]).name, - process.out.versions_minia, + process.out.findAll { key, val -> key.startsWith('versions') } ).match() } ) From d2652b86b8abd1d9f5992e27910b733a60bfea0a Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Fri, 27 Mar 2026 15:58:48 +0000 Subject: [PATCH 09/20] Update modules/nf-core/minia/main.nf MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/minia/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index ea112297c4fd..608653920249 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -15,7 +15,7 @@ process MINIA { tuple val(meta), path('*.unitigs.fa.gz'), emit: unitigs tuple val(meta), path('*.h5') , emit: h5 tuple val(meta), path("*-minia.log") , emit: log - tuple val("${task.process}"), val("minia"), eval("minia -v | grep Minia | sed 's/Minia version //g'"), topic: versions, emit: versions_minia + tuple val("${task.process}"), val("minia"), eval("minia -v | sed -n 's/Minia version //p'"), topic: versions, emit: versions_minia when: task.ext.when == null || task.ext.when From 01fc2051827f293d72cae743686506864a5b035f Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Fri, 27 Mar 2026 16:37:46 +0000 Subject: [PATCH 10/20] snap update --- modules/nf-core/minia/tests/main.nf.test.snap | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/minia/tests/main.nf.test.snap b/modules/nf-core/minia/tests/main.nf.test.snap index e1f76dbaec4b..c64f8223bf7b 100644 --- a/modules/nf-core/minia/tests/main.nf.test.snap +++ b/modules/nf-core/minia/tests/main.nf.test.snap @@ -5,19 +5,21 @@ "test.unitigs.fa.gz", "test.h5", "test-minia.log", - [ - [ - "MINIA", - "minia", - "3.2.6" + { + "versions_minia": [ + [ + "MINIA", + "minia", + "3.2.5" + ] ] - ] + } ], "meta": { "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-27T11:51:29.253914507" + "timestamp": "2026-03-27T16:29:27.70699655" }, "sarscov2 - fastq - pe": { "content": [ @@ -29,7 +31,7 @@ [ "MINIA", "minia", - "3.2.6" + "3.2.5" ] ] ], @@ -37,7 +39,7 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-27T11:51:34.477805031" + "timestamp": "2026-03-27T16:29:33.61312516" }, "test-minia-stub": { "content": [ @@ -78,7 +80,7 @@ [ "MINIA", "minia", - "3.2.6" + "3.2.5" ] ], "contigs": [ @@ -117,7 +119,7 @@ [ "MINIA", "minia", - "3.2.6" + "3.2.5" ] ] } @@ -126,6 +128,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.4" }, - "timestamp": "2026-03-27T11:51:39.674097511" + "timestamp": "2026-03-27T16:29:38.952052332" } } \ No newline at end of file From a656411613cf697758e265f266e53823c61ab0ed Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Mon, 30 Mar 2026 08:19:19 +0100 Subject: [PATCH 11/20] Update modules/nf-core/minia/tests/main.nf.test MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/minia/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/tests/main.nf.test b/modules/nf-core/minia/tests/main.nf.test index a2c01ccafb71..1523f22273bb 100644 --- a/modules/nf-core/minia/tests/main.nf.test +++ b/modules/nf-core/minia/tests/main.nf.test @@ -68,7 +68,7 @@ nextflow_process { file(process.out.unitigs[0][1]).name, file(process.out.h5[0][1]).name, file(process.out.log[0][1]).name, - process.out.versions_minia, + process.out.findAll { key, val -> key.startsWith('versions') }, ).match() } ) From d0650b08e0f683e9540d077bb825fe7e94f5a2e3 Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Mon, 30 Mar 2026 08:19:29 +0100 Subject: [PATCH 12/20] Update modules/nf-core/minia/meta.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/minia/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/meta.yml b/modules/nf-core/minia/meta.yml index 31e85c7f59b5..d29cebc9ecab 100644 --- a/modules/nf-core/minia/meta.yml +++ b/modules/nf-core/minia/meta.yml @@ -81,7 +81,7 @@ output: - minia: type: string description: The name of the tool - - minia -v | grep Minia | sed 's/Minia version //g': + - minia -v | sed -n 's/Minia version //p': type: eval description: The expression to obtain the version of the tool topics: From 03e8861a38c1cd1f230ea07a4b348258685188b8 Mon Sep 17 00:00:00 2001 From: Lia Obinu <96196229+LiaOb21@users.noreply.github.com> Date: Mon, 30 Mar 2026 08:19:40 +0100 Subject: [PATCH 13/20] Update modules/nf-core/minia/meta.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/minia/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/meta.yml b/modules/nf-core/minia/meta.yml index d29cebc9ecab..bc6e67e8f6dc 100644 --- a/modules/nf-core/minia/meta.yml +++ b/modules/nf-core/minia/meta.yml @@ -92,7 +92,7 @@ topics: - minia: type: string description: The name of the tool - - minia -v | grep Minia | sed 's/Minia version //g': + - minia -v | sed -n 's/Minia version //p': type: eval description: The expression to obtain the version of the tool authors: From c42a09eb5e8da6e303bd560ca44a7fdc7019f4b9 Mon Sep 17 00:00:00 2001 From: LiaOb21 Date: Mon, 30 Mar 2026 11:10:47 +0100 Subject: [PATCH 14/20] updating environments to correctly point to the last bioconda build of version 3.2.6 --- modules/nf-core/minia/main.nf | 4 +- modules/nf-core/minia/tests/main.nf.test.snap | 38 ++++++++++--------- 2 files changed, 22 insertions(+), 20 deletions(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 608653920249..1d5d1f34d305 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,8 +4,8 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d1/d1127b772f97ea9d62cb853d174a8e82be7e8e8598933d49b2061cb0550e276f/data' : - 'community.wave.seqera.io/library/minia:3.2.6--92bae1756baab1ef' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a3d1f6e0ab4974d2bd48bdbbbc0f96dc353e86e06b44b7c7b33a82462c7cd5d4/data' : + 'community.wave.seqera.io/library/minia:3.2.6--7fd896fcd6b7ed99' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/minia/tests/main.nf.test.snap b/modules/nf-core/minia/tests/main.nf.test.snap index c64f8223bf7b..be400df14666 100644 --- a/modules/nf-core/minia/tests/main.nf.test.snap +++ b/modules/nf-core/minia/tests/main.nf.test.snap @@ -10,16 +10,16 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ] } ], + "timestamp": "2026-03-30T08:38:40.819046992", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:29:27.70699655" + } }, "sarscov2 - fastq - pe": { "content": [ @@ -27,19 +27,21 @@ "test.unitigs.fa.gz", "test.h5", "test-minia.log", - [ - [ - "MINIA", - "minia", - "3.2.5" + { + "versions_minia": [ + [ + "MINIA", + "minia", + "3.2.6" + ] ] - ] + } ], + "timestamp": "2026-03-30T08:38:55.382497644", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:29:33.61312516" + } }, "test-minia-stub": { "content": [ @@ -80,7 +82,7 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ], "contigs": [ @@ -119,15 +121,15 @@ [ "MINIA", "minia", - "3.2.5" + "3.2.6" ] ] } ], + "timestamp": "2026-03-30T08:39:11.428189324", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-03-27T16:29:38.952052332" + } } } \ No newline at end of file From 5bf3b31de04f7d638b1567d73b2fe44737933b86 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 30 Mar 2026 12:36:27 +0200 Subject: [PATCH 15/20] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/nf-core/minia/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 1d5d1f34d305..608653920249 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,8 +4,8 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a3d1f6e0ab4974d2bd48bdbbbc0f96dc353e86e06b44b7c7b33a82462c7cd5d4/data' : - 'community.wave.seqera.io/library/minia:3.2.6--7fd896fcd6b7ed99' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d1/d1127b772f97ea9d62cb853d174a8e82be7e8e8598933d49b2061cb0550e276f/data' : + 'community.wave.seqera.io/library/minia:3.2.6--92bae1756baab1ef' }" input: tuple val(meta), path(reads) From d85c9b4cda2033b5d1488b38910815ee64da222e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Mar 2026 13:18:15 +0200 Subject: [PATCH 16/20] rebuild seqera container via CLI --- modules/nf-core/minia/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 1d5d1f34d305..d4c89c8196f2 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,8 +4,8 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a3d1f6e0ab4974d2bd48bdbbbc0f96dc353e86e06b44b7c7b33a82462c7cd5d4/data' : - 'community.wave.seqera.io/library/minia:3.2.6--7fd896fcd6b7ed99' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e8/e81f3434dbaa7e70bc0d11dbdf149efbf157955376d2f93e02e3be7dc3656101/data' : + 'community.wave.seqera.io/library/minia:3.2.6--5ceb3664bb860bc7' }" input: tuple val(meta), path(reads) From 22c3d7511f095f6c7293b5ab6a879cb46518b9a0 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Mar 2026 13:49:56 +0200 Subject: [PATCH 17/20] pin specific build and rebuild seqera containers --- modules/nf-core/minia/environment.yml | 2 +- modules/nf-core/minia/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/minia/environment.yml b/modules/nf-core/minia/environment.yml index 42eb2644eef5..fa6b5eb89992 100644 --- a/modules/nf-core/minia/environment.yml +++ b/modules/nf-core/minia/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::minia=3.2.6 + - bioconda::minia=3.2.6=h22625ea_6 diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index d4c89c8196f2..945575ebcf2b 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,8 +4,8 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e8/e81f3434dbaa7e70bc0d11dbdf149efbf157955376d2f93e02e3be7dc3656101/data' : - 'community.wave.seqera.io/library/minia:3.2.6--5ceb3664bb860bc7' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6a/6a92cc6d9541065f69e86af0bec39ed6cfaaa94085c0f50032af5ed6f35e37b8/data' : + 'community.wave.seqera.io/library/minia:3.2.6--df502ab09998dab4' }" input: tuple val(meta), path(reads) From a4bfd929d2a9c77c8d1b41f2b3cb2e8fe4107ab4 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Mar 2026 14:43:48 +0200 Subject: [PATCH 18/20] try again previous singularity URL --- modules/nf-core/minia/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 945575ebcf2b..d85e5e88c26c 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,7 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6a/6a92cc6d9541065f69e86af0bec39ed6cfaaa94085c0f50032af5ed6f35e37b8/data' : + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a3d1f6e0ab4974d2bd48bdbbbc0f96dc353e86e06b44b7c7b33a82462c7cd5d4/data' : 'community.wave.seqera.io/library/minia:3.2.6--df502ab09998dab4' }" input: From a2dec9a2f7661cab9b6f36ae5ab023b3c0e1f4a2 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Mar 2026 15:21:21 +0200 Subject: [PATCH 19/20] build singularity container once more (with default template) --- modules/nf-core/minia/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index d85e5e88c26c..018f190ea49d 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,7 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a3/a3d1f6e0ab4974d2bd48bdbbbc0f96dc353e86e06b44b7c7b33a82462c7cd5d4/data' : + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/40/40a4c0032d52284f76044828f50750948f2717e63f084e1ea80f6bd068b65b25/data' : 'community.wave.seqera.io/library/minia:3.2.6--df502ab09998dab4' }" input: From adbe01431f8b10ba8b34d738cb95c84b16058f35 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 30 Mar 2026 15:56:29 +0200 Subject: [PATCH 20/20] fix URL --- modules/nf-core/minia/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/minia/main.nf b/modules/nf-core/minia/main.nf index 018f190ea49d..4821ac28ca1a 100644 --- a/modules/nf-core/minia/main.nf +++ b/modules/nf-core/minia/main.nf @@ -4,7 +4,7 @@ process MINIA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/40/40a4c0032d52284f76044828f50750948f2717e63f084e1ea80f6bd068b65b25/data' : + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/40/40a4c0032d52284f76044828f50750948f2717e63f084e1ea80f6bd068b65b25/data' : 'community.wave.seqera.io/library/minia:3.2.6--df502ab09998dab4' }" input: