From c758b8fb92d92954b825d6d7fb059ef9e591a4ff Mon Sep 17 00:00:00 2001 From: EfraMP Date: Thu, 26 Mar 2026 15:51:17 -0600 Subject: [PATCH 1/3] bump versions and topics migration --- .../foldmason/createdb/environment.yml | 2 +- modules/nf-core/foldmason/createdb/main.nf | 16 ++-------- modules/nf-core/foldmason/createdb/meta.yml | 31 +++++++++++++------ .../nf-core/foldmason/easymsa/environment.yml | 2 +- modules/nf-core/foldmason/easymsa/main.nf | 4 +-- .../foldmason/msa2lddtreport/environment.yml | 2 +- .../nf-core/foldmason/msa2lddtreport/main.nf | 17 +++------- .../nf-core/foldmason/msa2lddtreport/meta.yml | 30 +++++++++++++----- 8 files changed, 56 insertions(+), 48 deletions(-) diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml index 9d5d3b05d0f9..02b2e756a855 100644 --- a/modules/nf-core/foldmason/createdb/environment.yml +++ b/modules/nf-core/foldmason/createdb/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::foldmason=2.7bd21ed + - bioconda::foldmason=4.dd3c235-0 diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf index 07b91d9ec93c..7b7c992693ce 100644 --- a/modules/nf-core/foldmason/createdb/main.nf +++ b/modules/nf-core/foldmason/createdb/main.nf @@ -4,15 +4,15 @@ process FOLDMASON_CREATEDB { 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/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' : - 'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dc0b27a73277c851f0a1df09fc5fa4f0ff80832e6779f143420a7e2321ac62b4/data' : + 'community.wave.seqera.io/library/foldmason:4.dd3c235--375019dcc3c5fe6f' }" input: tuple val(meta) , path(structures) output: tuple val(meta), path("${prefix}*"), emit: db - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('foldmason'), eval('foldmason version'), emit: versions_foldmason, topic: versions when: task.ext.when == null || task.ext.when @@ -26,21 +26,11 @@ process FOLDMASON_CREATEDB { ${prefix} \\ $args \\ --threads $task.cpus - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}') - END_VERSIONS """ stub: prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}') - END_VERSIONS """ } diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/modules/nf-core/foldmason/createdb/meta.yml index 311b82a2227c..04766448400e 100644 --- a/modules/nf-core/foldmason/createdb/meta.yml +++ b/modules/nf-core/foldmason/createdb/meta.yml @@ -12,9 +12,9 @@ tools: documentation: "https://github.com/steineggerlab/foldmason" tool_dev_url: "https://github.com/steineggerlab/foldmason" doi: "10.1101/2024.08.01.606130" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:foldmason - input: - - meta: type: map @@ -25,7 +25,6 @@ input: type: file description: Input protein structures in `PDB` or `mmCIF` format. pattern: "*.{pdb,mmcif}" - ontologies: [] output: db: @@ -39,13 +38,27 @@ output: description: All database files created by Foldmason pattern: "*" ontologies: [] + versions_foldmason: + - - ${task.process}: + type: string + description: The name of the process + - foldmason: + type: string + description: The name of the tool + - foldmason version: + 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 + - - ${task.process}: + type: string + description: The name of the process + - foldmason: + type: string + description: The name of the tool + - foldmason version: + type: eval + description: The expression to obtain the version of the tool authors: - "@luisas" maintainers: diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml index 7462add66871..7d7140592f88 100644 --- a/modules/nf-core/foldmason/easymsa/environment.yml +++ b/modules/nf-core/foldmason/easymsa/environment.yml @@ -4,5 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::foldmason=2.7bd21ed + - bioconda::foldmason=4.dd3c235-0 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf index f8feb9e3d1bc..ca268f1f1497 100644 --- a/modules/nf-core/foldmason/easymsa/main.nf +++ b/modules/nf-core/foldmason/easymsa/main.nf @@ -4,8 +4,8 @@ process FOLDMASON_EASYMSA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/067e6389ab95497b753ba1deabaa6acbce25b99c8cfcf39c06d5c1af42fd7751/data': - 'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/29/299b6d1a8a81632118e9c0cd110f9d89aae58b5a0132543a7fedbecb656da570/data': + 'community.wave.seqera.io/library/foldmason_pigz:289a5a7a978299df' }" input: diff --git a/modules/nf-core/foldmason/msa2lddtreport/environment.yml b/modules/nf-core/foldmason/msa2lddtreport/environment.yml index 9d5d3b05d0f9..02b2e756a855 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/environment.yml +++ b/modules/nf-core/foldmason/msa2lddtreport/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::foldmason=2.7bd21ed + - bioconda::foldmason=4.dd3c235-0 diff --git a/modules/nf-core/foldmason/msa2lddtreport/main.nf b/modules/nf-core/foldmason/msa2lddtreport/main.nf index 3ced3e709a86..c77e82db665e 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/main.nf +++ b/modules/nf-core/foldmason/msa2lddtreport/main.nf @@ -4,8 +4,8 @@ process FOLDMASON_MSA2LDDTREPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' : - 'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/dc/dc0b27a73277c851f0a1df09fc5fa4f0ff80832e6779f143420a7e2321ac62b4/data' : + 'community.wave.seqera.io/library/foldmason:4.dd3c235--375019dcc3c5fe6f' }" input: tuple val(meta) , path(msa) tuple val(meta2), path(db) @@ -14,7 +14,8 @@ process FOLDMASON_MSA2LDDTREPORT { output: tuple val(meta), path("${prefix}.html"), emit: html - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('foldmason'), eval('foldmason version'), emit: versions_foldmason, topic: versions + when: task.ext.when == null || task.ext.when @@ -31,21 +32,11 @@ process FOLDMASON_MSA2LDDTREPORT { $args \\ ${options_tree} \\ --threads $task.cpus - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}') - END_VERSIONS """ stub: prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}') - END_VERSIONS """ } diff --git a/modules/nf-core/foldmason/msa2lddtreport/meta.yml b/modules/nf-core/foldmason/msa2lddtreport/meta.yml index 1e74046c8bbb..ecb3d47ba003 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/meta.yml +++ b/modules/nf-core/foldmason/msa2lddtreport/meta.yml @@ -12,9 +12,9 @@ tools: documentation: "https://github.com/steineggerlab/foldmason" tool_dev_url: "https://github.com/steineggerlab/foldmason" doi: "10.1101/2024.08.01.606130" - licence: ["GPL v3"] + licence: + - "GPL v3" identifier: biotools:foldmason - input: - - meta: type: map @@ -68,13 +68,27 @@ output: description: HTML file with the foldmason visualization pattern: "*.{html}" ontologies: [] + versions_foldmason: + - - ${task.process}: + type: string + description: The name of the process + - foldmason: + type: string + description: The name of the tool + - foldmason version: + 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 + - foldmason: + type: string + description: The name of the tool + - foldmason version: + type: eval + description: The expression to obtain the version of the tool authors: - "@luisas" maintainers: From 645f55b79931b27d2da5542d64fa68e36506bf58 Mon Sep 17 00:00:00 2001 From: EfraMP Date: Thu, 26 Mar 2026 19:59:05 -0600 Subject: [PATCH 2/3] Update snapshots --- .../createdb/tests/main.nf.test.snap | 44 +++++++++++++------ .../msa2lddtreport/tests/main.nf.test | 4 +- .../msa2lddtreport/tests/main.nf.test.snap | 40 +++++++++++------ 3 files changed, 58 insertions(+), 30 deletions(-) diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap index dce5175dc90e..0769bab9d91b 100644 --- a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap +++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap @@ -26,7 +26,11 @@ ] ], "1": [ - "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + [ + "FOLDMASON_CREATEDB", + "foldmason", + "4.dd3c235" + ] ], "db": [ [ @@ -51,16 +55,20 @@ ] ] ], - "versions": [ - "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + "versions_foldmason": [ + [ + "FOLDMASON_CREATEDB", + "foldmason", + "4.dd3c235" + ] ] } ], + "timestamp": "2026-03-26T19:09:16.242972", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-09T15:11:27.426024133" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "seatoxin": { "content": [ @@ -89,7 +97,11 @@ ] ], "1": [ - "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + [ + "FOLDMASON_CREATEDB", + "foldmason", + "4.dd3c235" + ] ], "db": [ [ @@ -114,15 +126,19 @@ ] ] ], - "versions": [ - "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45" + "versions_foldmason": [ + [ + "FOLDMASON_CREATEDB", + "foldmason", + "4.dd3c235" + ] ] } ], + "timestamp": "2026-03-26T19:09:08.916379", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-09T15:11:15.375341633" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test index 945b4025b962..489db736ce91 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test +++ b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test @@ -67,7 +67,7 @@ nextflow_process { assertAll( { assert process.success }, { assert file(process.out.html.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } @@ -94,7 +94,7 @@ nextflow_process { assertAll( { assert process.success }, { assert file(process.out.html.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() } ) } diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap index 6e919329820a..d2c0b53964b0 100644 --- a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap +++ b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap @@ -1,26 +1,38 @@ { "seatoxin - stub": { "content": [ - [ - "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468" - ] + { + "versions_foldmason": [ + [ + "FOLDMASON_MSA2LDDTREPORT", + "foldmason", + "4.dd3c235" + ] + ] + } ], + "timestamp": "2026-03-26T19:25:18.035749", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-10T09:36:23.360594258" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "seatoxin": { "content": [ - [ - "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468" - ] + { + "versions_foldmason": [ + [ + "FOLDMASON_MSA2LDDTREPORT", + "foldmason", + "4.dd3c235" + ] + ] + } ], + "timestamp": "2026-03-26T19:25:03.917573", "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.2" - }, - "timestamp": "2024-12-10T09:54:03.711567262" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From 921548acd2d7d7c3b1a3ae748b7516a140572afb Mon Sep 17 00:00:00 2001 From: EfraMP Date: Thu, 26 Mar 2026 20:40:26 -0600 Subject: [PATCH 3/3] Update easymsa snapshot --- .../foldmason/easymsa/tests/main.nf.test.snap | 72 +++++++++---------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap index 98658d59c706..02878e35bbd7 100644 --- a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap +++ b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap @@ -22,7 +22,7 @@ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "3": [ @@ -52,7 +52,7 @@ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "versions_pigz": [ @@ -64,11 +64,11 @@ ] } ], + "timestamp": "2026-03-26T20:39:03.320607", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T17:44:34.671435974" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Test on seatoxin dataset - uncompressed": { "content": [ @@ -78,7 +78,7 @@ { "id": "test" }, - "test_3di.fa:md5,e7da437c6ddb5ced60ff7c49b147a65d" + "test_3di.fa:md5,87b7cb32dc09bc44f5700485c4c04944" ] ], "1": [ @@ -86,14 +86,14 @@ { "id": "test" }, - "test_aa.fa:md5,2d90cd080424db8024e6c404c1cfc0b4" + "test_aa.fa:md5,65cd0c4b10f37d6e17f7c52bd64a7bf5" ] ], "2": [ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "3": [ @@ -108,7 +108,7 @@ { "id": "test" }, - "test_3di.fa:md5,e7da437c6ddb5ced60ff7c49b147a65d" + "test_3di.fa:md5,87b7cb32dc09bc44f5700485c4c04944" ] ], "msa_aa": [ @@ -116,14 +116,14 @@ { "id": "test" }, - "test_aa.fa:md5,2d90cd080424db8024e6c404c1cfc0b4" + "test_aa.fa:md5,65cd0c4b10f37d6e17f7c52bd64a7bf5" ] ], "versions_foldmason": [ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "versions_pigz": [ @@ -135,11 +135,11 @@ ] } ], + "timestamp": "2026-03-26T20:38:35.039933", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T17:44:06.77699178" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Test on seatoxin dataset - compressed": { "content": [ @@ -149,7 +149,7 @@ { "id": "test" }, - "test_3di.fa.gz:md5,e7da437c6ddb5ced60ff7c49b147a65d" + "test_3di.fa.gz:md5,87b7cb32dc09bc44f5700485c4c04944" ] ], "1": [ @@ -157,14 +157,14 @@ { "id": "test" }, - "test_aa.fa.gz:md5,2d90cd080424db8024e6c404c1cfc0b4" + "test_aa.fa.gz:md5,65cd0c4b10f37d6e17f7c52bd64a7bf5" ] ], "2": [ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "3": [ @@ -179,7 +179,7 @@ { "id": "test" }, - "test_3di.fa.gz:md5,e7da437c6ddb5ced60ff7c49b147a65d" + "test_3di.fa.gz:md5,87b7cb32dc09bc44f5700485c4c04944" ] ], "msa_aa": [ @@ -187,14 +187,14 @@ { "id": "test" }, - "test_aa.fa.gz:md5,2d90cd080424db8024e6c404c1cfc0b4" + "test_aa.fa.gz:md5,65cd0c4b10f37d6e17f7c52bd64a7bf5" ] ], "versions_foldmason": [ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "versions_pigz": [ @@ -206,11 +206,11 @@ ] } ], + "timestamp": "2026-03-26T20:38:45.283399", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T17:44:16.0193125" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "Test on seatoxin dataset - guide_tree": { "content": [ @@ -220,7 +220,7 @@ { "id": "test" }, - "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08" + "test_3di.fa:md5,05af06303d43b84ba540e8a85957f789" ] ], "1": [ @@ -228,14 +228,14 @@ { "id": "test" }, - "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731" + "test_aa.fa:md5,ce75ecef9390218147cac9da63202ef7" ] ], "2": [ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "3": [ @@ -250,7 +250,7 @@ { "id": "test" }, - "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08" + "test_3di.fa:md5,05af06303d43b84ba540e8a85957f789" ] ], "msa_aa": [ @@ -258,14 +258,14 @@ { "id": "test" }, - "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731" + "test_aa.fa:md5,ce75ecef9390218147cac9da63202ef7" ] ], "versions_foldmason": [ [ "FOLDMASON_EASYMSA", "foldmason", - "2.7bd21ed" + "4.dd3c235" ] ], "versions_pigz": [ @@ -277,10 +277,10 @@ ] } ], + "timestamp": "2026-03-26T20:38:53.683563", "meta": { - "nf-test": "0.9.3", - "nextflow": "25.10.3" - }, - "timestamp": "2026-02-02T17:44:25.105523548" + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file